Datamonkey API (1.2.0)

Download OpenAPI specification:

E-mail: spond@temple.edu URL: http://github.com/veg/api-datamonkey License: Apache 2.0

Datamonkey is a free public server for comparative analysis of sequence alignments using state-of-the-art statistical models.
This is the OpenAPI definition for the Datamonkey API.

Use Datamonkey today!

Health

Check health of Datamonkey server

Check health of Datamonkey

query Parameters

pretty_print

boolean

Pretty print response

Responses

Response samples

200
500
503

Content type

application/json

{"status": "healthy",
"details": {"job_scheduler": "healthy",
"datamonkey": "healthy",
"llm": "healthy",
"database": "healthy"
}
}

Chat

Chat with an AI assistant to analyze data and run HyPhy methods

List conversations for the authenticated user

header Parameters

user_token

required

string

Token identifying the user

Responses

Response samples

200
401

Content type

application/json

{"conversations": [{"id": "string",
"title": "string",
"created": 0,
"updated": 0,
"messages": [{"role": "user",
"content": "string",
"timestamp": 0
}
]
}
]
}

Create a new conversation

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
optional

title

string

Optional title for the conversation

Responses

Request samples

Payload

Content type

application/json

{"title": "string"
}

Response samples

201
401

Content type

application/json

{"id": "string",
"title": "string",
"created": 0,
"updated": 0,
"messages": [{"role": "user",
"content": "string",
"timestamp": 0
}
]
}

Get a conversation by ID

path Parameters

conversationId

required

string

ID of the conversation

header Parameters

user_token

required

string

Token identifying the user

Responses

Response samples

200
401
403
404

Content type

application/json

{"id": "string",
"title": "string",
"created": 0,
"updated": 0,
"messages": [{"role": "user",
"content": "string",
"timestamp": 0
}
]
}

Delete a conversation

path Parameters

conversationId

required

string

ID of the conversation

header Parameters

user_token

required

string

Token identifying the user

Responses

Response samples

401
403
404

Content type

application/json

{"code": 401,
"message": "Unauthorized: Invalid or missing user token"
}

Get messages from a conversation

path Parameters

conversationId

required

string

ID of the conversation

header Parameters

user_token

required

string

Token identifying the user

Responses

Response samples

200
401
403
404

Content type

application/json

{"messages": [{"role": "user",
"content": "string",
"timestamp": 0
}
]
}

Send a message to the conversation

path Parameters

conversationId

required

string

ID of the conversation

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

message

required

string

Message content to send

Responses

Request samples

Payload

Content type

application/json

{"message": "string"
}

Response samples

200
401
403
404

Content type

application/json

{"message": {"role": "user",
"content": "string",
"timestamp": 0
}
}

File Upload and QC

Examples uploading files to Datamonkey

Get a list of datasets uploaded to Datamonkey

Get a list of datasets with optional filtering by user token

query Parameters

pretty_print	boolean Pretty print response
user_token	string Filter datasets by user token

Responses

Response samples

200
401

Content type

application/json

{"datasets": [{"name": "string",
"description": "string",
"type": "string",
"id": "string",
"user_token": "string",
"created": "2019-08-24T14:15:22Z",
"updated": "2019-08-24T14:15:22Z"
}
]
}

Upload a dataset to Datamonkey

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: multipart/form-data
required

	object (DatasetMeta)
user_token	string Token identifying the user who is uploading the dataset
file	string <binary> Dataset File. incompatible with the url field
url	string URL of the file to upload. incompatible with the file field

Responses

Response samples

201
401
422
500

Content type

application/json

{"datasets": [{"name": "string",
"description": "string",
"type": "string",
"id": "string",
"user_token": "string",
"created": "2019-08-24T14:15:22Z",
"updated": "2019-08-24T14:15:22Z"
}
]
}

Get details for a specific dataset

Get detailed information about a specific dataset

path Parameters

datasetId

required

string (Hash) ^[a-zA-Z0-9]+$

ID of the dataset to retrieve

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required if dataset is private)

Responses

Response samples

200
401
404
500

Content type

application/json

{"name": "string",
"description": "string",
"type": "string",
"id": "string",
"user_token": "string",
"created": "2019-08-24T14:15:22Z",
"updated": "2019-08-24T14:15:22Z"
}

Delete a dataset

Delete a dataset from the Datamonkey server

path Parameters

datasetId

required

string (Hash) ^[a-zA-Z0-9]+$

ID of the dataset to retrieve

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user who owns the dataset

Responses

Response samples

401
403
404
500

Content type

application/json

{"code": 401,
"message": "Unauthorized: Invalid or missing user token"
}

Jobs

Manage analysis jobs

Get a list of jobs

Get a list of jobs with optional filtering by user token, alignment ID, and/or tree ID

query Parameters

pretty_print	boolean Pretty print response
user_token	string Filter jobs by user token
alignment_id	string (Hash) ^[a-zA-Z0-9]+$ Filter jobs by alignment dataset ID
tree_id	string (Hash) ^[a-zA-Z0-9]+$ Filter jobs by tree dataset ID
method	string Filter jobs by HyPhy method
status	string Enum: "queued" "running" "completed" "error" Filter jobs by status

Responses

Response samples

200
401
500

Content type

application/json

{"jobs": [{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}
]
}

Get details for a specific job

Get detailed information about a specific job

path Parameters

jobId

required

string (Hash) ^[a-zA-Z0-9]+$

ID of the job

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required if job is private)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Delete a job

Delete a job from the Datamonkey server. If the job is running, it will be cancelled.

path Parameters

jobId

required

string (Hash) ^[a-zA-Z0-9]+$

ID of the job

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user who owns the job

Responses

Response samples

401
403
404
500

Content type

application/json

{"code": 401,
"message": "Unauthorized: Invalid or missing user token"
}

Methods

List and manage available HyPhy methods

Get a list of available HyPhy methods

Returns a list of all available HyPhy methods that can be run on the server

query Parameters

pretty_print

boolean

Pretty print response

Responses

Response samples

200
500

Content type

application/json

{"methods": [{"id": "string",
"name": "string",
"description": "string",
"status": "available",
"start_endpoint": "string",
"result_endpoint": "string",
"parameters": [{"name": "string",
"description": "string",
"required": true,
"type": "string",
"default": "string"
}
]
}
]
}

FEL

Examples starting jobs and fetching results for FEL

Start and monitor a FEL job

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
ci	string Default: "No" Enum: "Yes" "No" Compute confidence intervals for estimated rates
srv	string Default: "Yes" Enum: "Yes" "No" Include synonymous rate variation in the model
resample	number Default: 0 Number of bootstrap resamples
multiple_hits	string Default: "None" Enum: "None" "Double" "Double+Triple" Specify handling of multiple nucleotide substitutions
site_multihit	string Default: "Estimate" Enum: "Estimate" "Global" Specify whether to estimate multiple hit rates for each site
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
branches	Array of strings Default: [] Branches to include in the analysis. If empty, all branches are included.

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"ci": "Yes",
"srv": "Yes",
"resample": 0,
"multiple_hits": "None",
"site_multihit": "Estimate",
"genetic_code": "Universal",
"branches": [ ]
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a FEL job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"property2": {"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
}
},
"branch attributes": {"additionalProperties": {"property1": {"Global MG94xREV": 0,
"Nucleotide GTR": 0,
"original name": "string"
},
"property2": {"Global MG94xREV": 0,
"Nucleotide GTR": 0,
"original name": "string"
}
},
"attributes": {"property1": {"attribute type": "string",
"display order": 0
},
"property2": {"attribute type": "string",
"display order": 0
}
}
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": [[0
]
],
"property2": [[0
]
]
}
}
}
}

Get a FEL job result

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
ci	string Default: "No" Enum: "Yes" "No" Compute confidence intervals for estimated rates
srv	string Default: "Yes" Enum: "Yes" "No" Include synonymous rate variation in the model
resample	number Default: 0 Number of bootstrap resamples
multiple_hits	string Default: "None" Enum: "None" "Double" "Double+Triple" Specify handling of multiple nucleotide substitutions
site_multihit	string Default: "Estimate" Enum: "Estimate" "Global" Specify whether to estimate multiple hit rates for each site
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
branches	Array of strings Default: [] Branches to include in the analysis. If empty, all branches are included.

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"ci": "Yes",
"srv": "Yes",
"resample": 0,
"multiple_hits": "None",
"site_multihit": "Estimate",
"genetic_code": "Universal",
"branches": [ ]
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"property2": {"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
}
},
"branch attributes": {"additionalProperties": {"property1": {"Global MG94xREV": 0,
"Nucleotide GTR": 0,
"original name": "string"
},
"property2": {"Global MG94xREV": 0,
"Nucleotide GTR": 0,
"original name": "string"
}
},
"attributes": {"property1": {"attribute type": "string",
"display order": 0
},
"property2": {"attribute type": "string",
"display order": 0
}
}
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": [[0
]
],
"property2": [[0
]
]
}
}
}
}

BUSTED

Examples starting jobs and fetching results for BUSTED

Start and monitor a BUSTED job

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
srv	string Default: "Yes" Enum: "Yes" "No" "branch-site" Include synonymous rate variation in the model
multiple_hits	string Default: "None" Enum: "None" "Double" "Double+Triple" Specify handling of multiple nucleotide substitutions
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
branches	Array of strings Default: [] Branches to include in the analysis. If empty, all branches are included.
rates	integer [ 1 .. 10 ] Default: 3 The number omega rate classes to include in the model
syn_rates	integer [ 1 .. 10 ] Default: 3 The number synonymous rate classes to include in the model
grid_size	integer >= 1 Default: 250 The number of points in the initial distributional guess for likelihood fitting
starting_points	integer >= 1 Default: 1 The number of initial random guesses to seed rate values optimization
error_sink	string Default: "No" Enum: "Yes" "No" An advanced experimental setting; include a rate class to capture misalignment artifacts

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"srv": "Yes",
"multiple_hits": "None",
"genetic_code": "Universal",
"branches": [ ],
"rates": 3,
"syn_rates": 3,
"grid_size": 250,
"starting_points": 1,
"error_sink": "Yes"
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a BUSTED job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"background": 0,
"fits": {"property1": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"property2": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
}
},
"branch attributes": {"additionalProperties": {"property1": {"MG94xREV with separate rates for branch sets": 0,
"Nucleotide GTR": 0,
"Posterior prob omega class": [[0
]
],
"Posterior prob omega class by site": [[0
]
],
"constrained": 0,
"original name": "string",
"unconstrained": 0
},
"property2": {"MG94xREV with separate rates for branch sets": 0,
"Nucleotide GTR": 0,
"Posterior prob omega class": [[0
]
],
"Posterior prob omega class by site": [[0
]
],
"constrained": 0,
"original name": "string",
"unconstrained": 0
}
},
"attributes": {"property1": {"attribute type": "string",
"display order": 0
},
"property2": {"attribute type": "string",
"display order": 0
}
}
},
"test results": {"LRT": 0,
"p-value": 0
},
"substitutions": {"property1": {"property1": {"root": "string",
"property1": "string",
"property2": "string"
},
"property2": {"root": "string",
"property1": "string",
"property2": "string"
}
},
"property2": {"property1": {"root": "string",
"property1": "string",
"property2": "string"
},
"property2": {"root": "string",
"property1": "string",
"property2": "string"
}
}
},
"Synonymous site-posteriors": [[0
]
],
"Site Log Likelihood": {"constrained": [[0
]
],
"unconstrained": [[0
]
],
"optimized null": [[0
]
]
},
"Evidence Ratios": {"constrained": [[0
]
],
"optimized null": [[0
]
]
}
}
}

Get a BUSTED job result

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
srv	string Default: "Yes" Enum: "Yes" "No" "branch-site" Include synonymous rate variation in the model
multiple_hits	string Default: "None" Enum: "None" "Double" "Double+Triple" Specify handling of multiple nucleotide substitutions
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
branches	Array of strings Default: [] Branches to include in the analysis. If empty, all branches are included.
rates	integer [ 1 .. 10 ] Default: 3 The number omega rate classes to include in the model
syn_rates	integer [ 1 .. 10 ] Default: 3 The number synonymous rate classes to include in the model
grid_size	integer >= 1 Default: 250 The number of points in the initial distributional guess for likelihood fitting
starting_points	integer >= 1 Default: 1 The number of initial random guesses to seed rate values optimization
error_sink	string Default: "No" Enum: "Yes" "No" An advanced experimental setting; include a rate class to capture misalignment artifacts

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"srv": "Yes",
"multiple_hits": "None",
"genetic_code": "Universal",
"branches": [ ],
"rates": 3,
"syn_rates": 3,
"grid_size": 250,
"starting_points": 1,
"error_sink": "Yes"
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"background": 0,
"fits": {"property1": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"property2": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
}
},
"branch attributes": {"additionalProperties": {"property1": {"MG94xREV with separate rates for branch sets": 0,
"Nucleotide GTR": 0,
"Posterior prob omega class": [[0
]
],
"Posterior prob omega class by site": [[0
]
],
"constrained": 0,
"original name": "string",
"unconstrained": 0
},
"property2": {"MG94xREV with separate rates for branch sets": 0,
"Nucleotide GTR": 0,
"Posterior prob omega class": [[0
]
],
"Posterior prob omega class by site": [[0
]
],
"constrained": 0,
"original name": "string",
"unconstrained": 0
}
},
"attributes": {"property1": {"attribute type": "string",
"display order": 0
},
"property2": {"attribute type": "string",
"display order": 0
}
}
},
"test results": {"LRT": 0,
"p-value": 0
},
"substitutions": {"property1": {"property1": {"root": "string",
"property1": "string",
"property2": "string"
},
"property2": {"root": "string",
"property1": "string",
"property2": "string"
}
},
"property2": {"property1": {"root": "string",
"property1": "string",
"property2": "string"
},
"property2": {"root": "string",
"property1": "string",
"property2": "string"
}
}
},
"Synonymous site-posteriors": [[0
]
],
"Site Log Likelihood": {"constrained": [[0
]
],
"unconstrained": [[0
]
],
"optimized null": [[0
]
]
},
"Evidence Ratios": {"constrained": [[0
]
],
"optimized null": [[0
]
]
}
}
}

ABSREL

Examples starting jobs and fetching results for ABSREL

Start and monitor an ABSREL job

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
srv	string Default: "Yes" Enum: "Yes" "No" Include synonymous rate variation in the model
multiple_hits	string Default: "None" Enum: "None" "Double" "Double+Triple" Specify handling of multiple nucleotide substitutions
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
branches	Array of strings Default: [] Branches to include in the analysis. If empty, all branches are included.
blb	number [ 0 .. 1 ] Default: 1 Bag of little bootstrap alignment resampling rate

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"srv": "Yes",
"multiple_hits": "None",
"genetic_code": "Universal",
"branches": [ ],
"blb": 1
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get an ABSREL job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "string",
"property2": "string"
},
"property2": {"property1": "string",
"property2": "string"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0,
"Equilibrium frequencies": [[0
]
]
},
"property2": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0,
"Equilibrium frequencies": [[0
]
]
}
},
"test results": {"P-value threshold": 0,
"tested": 0,
"positive test results": 0
},
"branch attributes": {"additionalProperties": {"property1": {"original name": "string",
"Nucleotide GTR": 0,
"Baseline MG94xREV": 0,
"Baseline MG94xREV omega ratio": 0,
"Rate classes": 0,
"Full adaptive model": 0,
"Rate Distributions": [[0
]
],
"LRT": 0,
"Uncorrected P-value": 0,
"Corrected P-value": 0
},
"property2": {"original name": "string",
"Nucleotide GTR": 0,
"Baseline MG94xREV": 0,
"Baseline MG94xREV omega ratio": 0,
"Rate classes": 0,
"Full adaptive model": 0,
"Rate Distributions": [[0
]
],
"LRT": 0,
"Uncorrected P-value": 0,
"Corrected P-value": 0
}
},
"attributes": {"property1": {"attribute type": "string",
"display order": 0
},
"property2": {"attribute type": "string",
"display order": 0
}
}
}
}
}

Get an ABSREL job result

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
srv	string Default: "Yes" Enum: "Yes" "No" Include synonymous rate variation in the model
multiple_hits	string Default: "None" Enum: "None" "Double" "Double+Triple" Specify handling of multiple nucleotide substitutions
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
branches	Array of strings Default: [] Branches to include in the analysis. If empty, all branches are included.
blb	number [ 0 .. 1 ] Default: 1 Bag of little bootstrap alignment resampling rate

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"srv": "Yes",
"multiple_hits": "None",
"genetic_code": "Universal",
"branches": [ ],
"blb": 1
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "string",
"property2": "string"
},
"property2": {"property1": "string",
"property2": "string"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0,
"Equilibrium frequencies": [[0
]
]
},
"property2": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0,
"Equilibrium frequencies": [[0
]
]
}
},
"test results": {"P-value threshold": 0,
"tested": 0,
"positive test results": 0
},
"branch attributes": {"additionalProperties": {"property1": {"original name": "string",
"Nucleotide GTR": 0,
"Baseline MG94xREV": 0,
"Baseline MG94xREV omega ratio": 0,
"Rate classes": 0,
"Full adaptive model": 0,
"Rate Distributions": [[0
]
],
"LRT": 0,
"Uncorrected P-value": 0,
"Corrected P-value": 0
},
"property2": {"original name": "string",
"Nucleotide GTR": 0,
"Baseline MG94xREV": 0,
"Baseline MG94xREV omega ratio": 0,
"Rate classes": 0,
"Full adaptive model": 0,
"Rate Distributions": [[0
]
],
"LRT": 0,
"Uncorrected P-value": 0,
"Corrected P-value": 0
}
},
"attributes": {"property1": {"attribute type": "string",
"display order": 0
},
"property2": {"attribute type": "string",
"display order": 0
}
}
}
}
}

BGM

Examples starting jobs and fetching results for BGM (Bayesian Graphical Model)

Start and monitor a BGM job

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
branches	string Default: "All" Specify branches to test
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
data_type	string Default: "codon" Enum: "nucleotide" "amino-acid" "codon" The type of data being analyzed
steps	integer Default: 100000 Number of MCMC steps to sample
burn_in	integer Default: 10000 Number of MCMC steps to discard as burn-in
samples	integer Default: 100 Number of samples to extract from the chain
max_parents	integer Default: 1 Maximum number of parents allowed per node
min_subs	integer Default: 1 Minimum number of substitutions per site to include in the analysis

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"branches": "All",
"genetic_code": "Universal",
"data_type": "nucleotide",
"steps": 100000,
"burn_in": 10000,
"samples": 100,
"max_parents": 1,
"min_subs": 1
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a BGM job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Rate Distributions": { },
"display order": 0
},
"property2": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Rate Distributions": { },
"display order": 0
}
},
"MLE": {"headers": [["string"
]
],
"content": [[0
]
]
},
"branch attributes": {"property1": {"property1": {"property1": 0,
"property2": 0
},
"property2": {"property1": 0,
"property2": 0
}
},
"property2": {"property1": {"property1": 0,
"property2": 0
},
"property2": {"property1": 0,
"property2": 0
}
}
}
}
}

Get a BGM job result

query Parameters

pretty_print

boolean

Pretty print response

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
branches	string Default: "All" Specify branches to test
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
data_type	string Default: "codon" Enum: "nucleotide" "amino-acid" "codon" The type of data being analyzed
steps	integer Default: 100000 Number of MCMC steps to sample
burn_in	integer Default: 10000 Number of MCMC steps to discard as burn-in
samples	integer Default: 100 Number of samples to extract from the chain
max_parents	integer Default: 1 Maximum number of parents allowed per node
min_subs	integer Default: 1 Minimum number of substitutions per site to include in the analysis

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"branches": "All",
"genetic_code": "Universal",
"data_type": "nucleotide",
"steps": 100000,
"burn_in": 10000,
"samples": 100,
"max_parents": 1,
"min_subs": 1
}

Response samples

200
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Rate Distributions": { },
"display order": 0
},
"property2": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Rate Distributions": { },
"display order": 0
}
},
"MLE": {"headers": [["string"
]
],
"content": [[0
]
]
},
"branch attributes": {"property1": {"property1": {"property1": 0,
"property2": 0
},
"property2": {"property1": 0,
"property2": 0
}
},
"property2": {"property1": {"property1": 0,
"property2": 0
},
"property2": {"property1": 0,
"property2": 0
}
}
}
}
}

CONTRAST-FEL

Examples starting jobs and fetching results for CONTRAST-FEL (Fixed Effects Likelihood with Contrast)

Start a CONTRAST-FEL analysis

Starts a Contrast-FEL (Fixed Effects Likelihood with Contrast) job to investigate whether selective pressures differ between two or more sets of branches at a site. The method estimates site-specific synonymous (alpha) and non-synonymous (beta, one per branch set) substitution rates and tests beta rates for equality at each site.

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment required	string (Hash) ^[a-zA-Z0-9]+$
tree required	string (Hash) ^[a-zA-Z0-9]+$
branch_sets required	Array of strings Array of branch sets to be used for comparison (e.g., "Source" and "Test" groups)
genetic_code	string Default: "Universal" Which genetic code should be used
srv	string Default: "Yes" Include synonymous rate variation in the model ("Yes" or "No")
permutations	string Default: "Yes" Perform permutation significance tests ("Yes" or "No")
p_value	number Default: 0.05 Significance value for site tests
q_value	number Default: 0.2 Significance value for False Discovery Rate reporting

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"branch_sets": ["string"
],
"genetic_code": "Universal",
"srv": "Yes",
"permutations": "Yes",
"p_value": 0.05,
"q_value": 0.2
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get CONTRAST-FEL job result by job ID

query Parameters

job_id

required

string (Hash) ^[a-zA-Z0-9]+$

Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": "string",
"property2": "string"
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": [[0
]
],
"property2": [[0
]
]
}
},
"branch_attributes": {"property1": { },
"property2": { }
},
"fits": {"property1": { },
"property2": { }
}
}
}

Get CONTRAST-FEL analysis results

Retrieves the results of a previously submitted CONTRAST-FEL job. CONTRAST-FEL investigates whether selective pressures differ between two or more sets of branches at a site by estimating site-specific synonymous and non-synonymous substitution rates.

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment required	string (Hash) ^[a-zA-Z0-9]+$
tree required	string (Hash) ^[a-zA-Z0-9]+$
branch_sets required	Array of strings Array of branch sets to be used for comparison (e.g., "Source" and "Test" groups)
genetic_code	string Default: "Universal" Which genetic code should be used
srv	string Default: "Yes" Include synonymous rate variation in the model ("Yes" or "No")
permutations	string Default: "Yes" Perform permutation significance tests ("Yes" or "No")
p_value	number Default: 0.05 Significance value for site tests
q_value	number Default: 0.2 Significance value for False Discovery Rate reporting

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"branch_sets": ["string"
],
"genetic_code": "Universal",
"srv": "Yes",
"permutations": "Yes",
"p_value": 0.05,
"q_value": 0.2
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": "string",
"property2": "string"
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": [[0
]
],
"property2": [[0
]
]
}
},
"branch_attributes": {"property1": { },
"property2": { }
},
"fits": {"property1": { },
"property2": { }
}
}
}

FUBAR

Examples starting jobs and fetching results for FUBAR (Fast Unconstrained Bayesian AppRoximation)

Start a FUBAR analysis

Starts a Fast Unconstrained Bayesian AppRoximation (FUBAR) job to detect sites under positive selection. FUBAR uses a Bayesian approach to infer selection pressures at individual sites, providing posterior probabilities of positive and negative selection.

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment required	string (Hash) ^[a-zA-Z0-9]+$
tree required	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string Default: "Universal" Which genetic code should be used
grid_points	integer [ 5 .. 50 ] Default: 20 Number of grid points for the Bayesian analysis (must be between 5 and 50)
concentration_parameter	number [ 0.001 .. 1 ] Default: 0.5 Concentration parameter for the Dirichlet prior in the Bayesian estimation

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"genetic_code": "Universal",
"grid_points": 20,
"concentration_parameter": 0.5
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a FUBAR job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": { },
"property2": { }
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": [[0
]
],
"property2": [[0
]
]
}
},
"grid": [[0
]
]
}
}

Get FUBAR analysis results

Retrieves the results of a previously submitted Fast Unconstrained Bayesian AppRoximation (FUBAR) job. FUBAR uses a Bayesian approach to infer selection pressures at individual sites, providing posterior probabilities of positive and negative selection.

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment required	string (Hash) ^[a-zA-Z0-9]+$
tree required	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string Default: "Universal" Which genetic code should be used
grid_points	integer [ 5 .. 50 ] Default: 20 Number of grid points for the Bayesian analysis (must be between 5 and 50)
concentration_parameter	number [ 0.001 .. 1 ] Default: 0.5 Concentration parameter for the Dirichlet prior in the Bayesian estimation

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"genetic_code": "Universal",
"grid_points": 20,
"concentration_parameter": 0.5
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": { },
"property2": { }
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": [[0
]
],
"property2": [[0
]
]
}
},
"grid": [[0
]
]
}
}

GARD

Examples starting jobs and fetching results for GARD (Genetic Algorithm for Recombination Detection)

Start a GARD analysis

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
data_type	string Default: "Nucleotide" Enum: "Nucleotide" "Protein" The type of data being analyzed
run_mode	string Default: "Normal" Enum: "Normal" "Faster" The optimization mode
site_to_site_variation	string Default: "None" Enum: "None" "General Discrete" "Beta-Gamma" Specifies the model for rate variation among sites
rate_classes	integer Default: 2 The number of discrete rate classes for rate variation
model	string Default: "JTT" The substitution model to use

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"genetic_code": "Universal",
"data_type": "Nucleotide",
"run_mode": "Normal",
"site_to_site_variation": "None",
"rate_classes": 2,
"model": "JTT"
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a GARD job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"baselineScore": 0,
"potentialBreakpoints": 0,
"singleTreeAICc": 0,
"timeElapsed": 0,
"totalModelCount": 0,
"breakpointData": {"property1": {"bps": [[0
]
],
"tree": "string"
},
"property2": {"bps": [[0
]
],
"tree": "string"
}
},
"improvements": {"property1": {"breakpoints": [[0
]
],
"deltaAICc": 0
},
"property2": {"breakpoints": [[0
]
],
"deltaAICc": 0
}
},
"siteBreakPointSupport": {"property1": 0,
"property2": 0
},
"trees": {"property1": { },
"property2": { }
}
}
}

Get GARD analysis results

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
data_type	string Default: "Nucleotide" Enum: "Nucleotide" "Protein" The type of data being analyzed
run_mode	string Default: "Normal" Enum: "Normal" "Faster" The optimization mode
site_to_site_variation	string Default: "None" Enum: "None" "General Discrete" "Beta-Gamma" Specifies the model for rate variation among sites
rate_classes	integer Default: 2 The number of discrete rate classes for rate variation
model	string Default: "JTT" The substitution model to use

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"genetic_code": "Universal",
"data_type": "Nucleotide",
"run_mode": "Normal",
"site_to_site_variation": "None",
"rate_classes": 2,
"model": "JTT"
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"baselineScore": 0,
"potentialBreakpoints": 0,
"singleTreeAICc": 0,
"timeElapsed": 0,
"totalModelCount": 0,
"breakpointData": {"property1": {"bps": [[0
]
],
"tree": "string"
},
"property2": {"bps": [[0
]
],
"tree": "string"
}
},
"improvements": {"property1": {"breakpoints": [[0
]
],
"deltaAICc": 0
},
"property2": {"breakpoints": [[0
]
],
"deltaAICc": 0
}
},
"siteBreakPointSupport": {"property1": 0,
"property2": 0
},
"trees": {"property1": { },
"property2": { }
}
}
}

MEME

Examples starting jobs and fetching results for MEME (Mixed Effects Model of Evolution)

Start a MEME analysis

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
multiple_hits	string Default: "None" Enum: "None" "Double" "Double+Triple" Specify handling of multiple nucleotide substitutions
site_multihit	string Default: "Estimate" Enum: "Estimate" "Global" Specify whether to estimate multiple hit rates for each site
rates	integer Default: 2 Number of different categories of non-synonymous rates
resample	number Default: 0 Number of bootstrapping replicates
impute_states	string Default: "No" Enum: "Yes" "No" Option to impute likely character states for missing data

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"genetic_code": "Universal",
"multiple_hits": "None",
"site_multihit": "Estimate",
"rates": 2,
"resample": 0,
"impute_states": "Yes"
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a MEME job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"property2": {"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
}
},
"branch attributes": {"additionalProperties": {"property1": {"Global MG94xREV": 0,
"Nucleotide GTR": 0,
"original name": "string"
},
"property2": {"Global MG94xREV": 0,
"Nucleotide GTR": 0,
"original name": "string"
}
},
"attributes": {"property1": {"attribute type": "string",
"display order": 0
},
"property2": {"attribute type": "string",
"display order": 0
}
}
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": [[0
]
],
"property2": [[0
]
]
}
}
}
}

Get MEME analysis results

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
multiple_hits	string Default: "None" Enum: "None" "Double" "Double+Triple" Specify handling of multiple nucleotide substitutions
site_multihit	string Default: "Estimate" Enum: "Estimate" "Global" Specify whether to estimate multiple hit rates for each site
rates	integer Default: 2 Number of different categories of non-synonymous rates
resample	number Default: 0 Number of bootstrapping replicates
impute_states	string Default: "No" Enum: "Yes" "No" Option to impute likely character states for missing data

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"genetic_code": "Universal",
"multiple_hits": "None",
"site_multihit": "Estimate",
"rates": 2,
"resample": 0,
"impute_states": "Yes"
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"property2": {"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
}
},
"branch attributes": {"additionalProperties": {"property1": {"Global MG94xREV": 0,
"Nucleotide GTR": 0,
"original name": "string"
},
"property2": {"Global MG94xREV": 0,
"Nucleotide GTR": 0,
"original name": "string"
}
},
"attributes": {"property1": {"attribute type": "string",
"display order": 0
},
"property2": {"attribute type": "string",
"display order": 0
}
}
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": [[0
]
],
"property2": [[0
]
]
}
}
}
}

MULTI-HIT

Examples starting jobs and fetching results for MULTI-HIT (Multiple Hit) analysis

Start a MULTI-HIT analysis

MULTI-HIT (Multiple Hit) examines whether or not a codon alignment is better fit by models which permit multiple instantaneous substitutions. It can analyze both double-hit and triple-hit substitutions, with an option to account for synonymous triple-hit substitutions.

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment required	string (Hash) ^[a-zA-Z0-9]+$
genetic_code required	string Default: "Universal" The genetic code to use for the analysis
triple_islands	string Default: "No" Enum: "Yes" "No" Toggle for accounting synonymous triple-hit substitutions
rate_classes	integer [ 1 .. 10 ] Default: 3 Number of rate classes to use

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"genetic_code": "Universal",
"triple_islands": "Yes",
"rate_classes": 3
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a MULTI-HIT job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"Evidence Ratios": {"Three-hit": [[0
]
],
"Two-hit": [[0
]
],
"Three-hit islands vs 2-hit": [[0
]
]
},
"site_substitutions": {"property1": {"property1": { },
"property2": { }
},
"property2": {"property1": { },
"property2": { }
}
},
"fits": {"MG94 with double and triple instantaneous substitutions": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"MG94 with double and triple instantaneous substitutions only synonymous islands": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"MG94 with double instantaneous substitutions": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"Nucleotide GTR": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"Standard MG94": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
}
},
"test_results": {"Double hit vs single hit": {"LRT": 0,
"p-value": 0
},
"Triple hit vs Triple hit island": {"LRT": 0,
"p-value": 0
},
"Triple hit vs double hit": {"LRT": 0,
"p-value": 0
},
"Triple hit vs single hit": {"LRT": 0,
"p-value": 0
},
"Triple hit island vs double hit": {"LRT": 0,
"p-value": 0
}
}
}
}

Get MULTI-HIT analysis results

Retrieve the results of a previously submitted MULTI-HIT analysis job. Results include evidence ratios for different substitution types, site-specific substitutions, model fitting information, and statistical test results comparing different models.

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment required	string (Hash) ^[a-zA-Z0-9]+$
genetic_code required	string Default: "Universal" The genetic code to use for the analysis
triple_islands	string Default: "No" Enum: "Yes" "No" Toggle for accounting synonymous triple-hit substitutions
rate_classes	integer [ 1 .. 10 ] Default: 3 Number of rate classes to use

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"genetic_code": "Universal",
"triple_islands": "Yes",
"rate_classes": 3
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"Evidence Ratios": {"Three-hit": [[0
]
],
"Two-hit": [[0
]
],
"Three-hit islands vs 2-hit": [[0
]
]
},
"site_substitutions": {"property1": {"property1": { },
"property2": { }
},
"property2": {"property1": { },
"property2": { }
}
},
"fits": {"MG94 with double and triple instantaneous substitutions": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"MG94 with double and triple instantaneous substitutions only synonymous islands": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"MG94 with double instantaneous substitutions": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"Nucleotide GTR": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
},
"Standard MG94": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": { },
"display order": 0,
"estimated parameters": 0
}
},
"test_results": {"Double hit vs single hit": {"LRT": 0,
"p-value": 0
},
"Triple hit vs Triple hit island": {"LRT": 0,
"p-value": 0
},
"Triple hit vs double hit": {"LRT": 0,
"p-value": 0
},
"Triple hit vs single hit": {"LRT": 0,
"p-value": 0
},
"Triple hit island vs double hit": {"LRT": 0,
"p-value": 0
}
}
}
}

RELAX

Examples starting jobs and fetching results for RELAX (Hypothesis testing framework to detect relaxation of selection)

Start and monitor a RELAX job

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
test_branches	Array of strings Default: [] Branches to be considered as 'Test'
reference_branches	Array of strings Default: [] Branches to be considered as 'Reference'
models	string Default: "All" Enum: "All" "Minimal" Type of analysis to run (All for descriptive models and RELAX test, Minimal for only the RELAX test)
rates	integer Default: 3 Number of omega rate classes
kill_zero_lengths	string Default: "No" Enum: "Yes" "No" Specify whether to handle zero-length branches

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"genetic_code": "Universal",
"test_branches": [ ],
"reference_branches": [ ],
"models": "All",
"rates": 3,
"kill_zero_lengths": "Yes"
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a RELAX job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"Nucleotide GTR": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": {"property1": 0,
"property2": 0
},
"display order": 0
},
"MG94xREV with separate rates for branch sets": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": {"property1": [[0
]
],
"property2": [[0
]
]
},
"display order": 0
},
"General descriptive": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Rate Distributions": {"Shared": {"property1": {"omega": 0,
"proportion": 0
},
"property2": {"omega": 0,
"proportion": 0
}
}
},
"display order": 0
},
"RELAX alternative": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Rate Distributions": {"Test": {"property1": {"omega": 0,
"proportion": 0
},
"property2": {"omega": 0,
"proportion": 0
}
},
"Reference": {"property1": {"omega": 0,
"proportion": 0
},
"property2": {"omega": 0,
"proportion": 0
}
}
},
"display order": 0
},
"RELAX null": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Rate Distributions": {"Test": {"property1": {"omega": 0,
"proportion": 0
},
"property2": {"omega": 0,
"proportion": 0
}
},
"Reference": {"property1": {"omega": 0,
"proportion": 0
},
"property2": {"omega": 0,
"proportion": 0
}
}
},
"display order": 0
}
},
"test results": {"p-value": 0,
"relaxation or intensification parameter": 0,
"test": "string",
"alternative": "string",
"null": "string",
"background": "string",
"log likelihood ratio": 0,
"degrees of freedom": 0,
"branch attributes": {"property1": {"property1": {"original name": "string",
"Nucleotide GTR": 0,
"MG94xREV with separate rates for branch sets": 0,
"General descriptive": 0,
"k (general descriptive)": 0,
"RELAX null": 0,
"RELAX alternative": 0,
"k (RELAX alternative)": 0,
"tested": true
},
"property2": {"original name": "string",
"Nucleotide GTR": 0,
"MG94xREV with separate rates for branch sets": 0,
"General descriptive": 0,
"k (general descriptive)": 0,
"RELAX null": 0,
"RELAX alternative": 0,
"k (RELAX alternative)": 0,
"tested": true
}
},
"property2": {"property1": {"original name": "string",
"Nucleotide GTR": 0,
"MG94xREV with separate rates for branch sets": 0,
"General descriptive": 0,
"k (general descriptive)": 0,
"RELAX null": 0,
"RELAX alternative": 0,
"k (RELAX alternative)": 0,
"tested": true
},
"property2": {"original name": "string",
"Nucleotide GTR": 0,
"MG94xREV with separate rates for branch sets": 0,
"General descriptive": 0,
"k (general descriptive)": 0,
"RELAX null": 0,
"RELAX alternative": 0,
"k (RELAX alternative)": 0,
"tested": true
}
}
}
}
}
}

Get RELAX analysis results

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
test_branches	Array of strings Default: [] Branches to be considered as 'Test'
reference_branches	Array of strings Default: [] Branches to be considered as 'Reference'
models	string Default: "All" Enum: "All" "Minimal" Type of analysis to run (All for descriptive models and RELAX test, Minimal for only the RELAX test)
rates	integer Default: 3 Number of omega rate classes
kill_zero_lengths	string Default: "No" Enum: "Yes" "No" Specify whether to handle zero-length branches

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"genetic_code": "Universal",
"test_branches": [ ],
"reference_branches": [ ],
"models": "All",
"rates": 3,
"kill_zero_lengths": "Yes"
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"Nucleotide GTR": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": {"property1": 0,
"property2": 0
},
"display order": 0
},
"MG94xREV with separate rates for branch sets": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": {"property1": [[0
]
],
"property2": [[0
]
]
},
"display order": 0
},
"General descriptive": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Rate Distributions": {"Shared": {"property1": {"omega": 0,
"proportion": 0
},
"property2": {"omega": 0,
"proportion": 0
}
}
},
"display order": 0
},
"RELAX alternative": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Rate Distributions": {"Test": {"property1": {"omega": 0,
"proportion": 0
},
"property2": {"omega": 0,
"proportion": 0
}
},
"Reference": {"property1": {"omega": 0,
"proportion": 0
},
"property2": {"omega": 0,
"proportion": 0
}
}
},
"display order": 0
},
"RELAX null": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Rate Distributions": {"Test": {"property1": {"omega": 0,
"proportion": 0
},
"property2": {"omega": 0,
"proportion": 0
}
},
"Reference": {"property1": {"omega": 0,
"proportion": 0
},
"property2": {"omega": 0,
"proportion": 0
}
}
},
"display order": 0
}
},
"test results": {"p-value": 0,
"relaxation or intensification parameter": 0,
"test": "string",
"alternative": "string",
"null": "string",
"background": "string",
"log likelihood ratio": 0,
"degrees of freedom": 0,
"branch attributes": {"property1": {"property1": {"original name": "string",
"Nucleotide GTR": 0,
"MG94xREV with separate rates for branch sets": 0,
"General descriptive": 0,
"k (general descriptive)": 0,
"RELAX null": 0,
"RELAX alternative": 0,
"k (RELAX alternative)": 0,
"tested": true
},
"property2": {"original name": "string",
"Nucleotide GTR": 0,
"MG94xREV with separate rates for branch sets": 0,
"General descriptive": 0,
"k (general descriptive)": 0,
"RELAX null": 0,
"RELAX alternative": 0,
"k (RELAX alternative)": 0,
"tested": true
}
},
"property2": {"property1": {"original name": "string",
"Nucleotide GTR": 0,
"MG94xREV with separate rates for branch sets": 0,
"General descriptive": 0,
"k (general descriptive)": 0,
"RELAX null": 0,
"RELAX alternative": 0,
"k (RELAX alternative)": 0,
"tested": true
},
"property2": {"original name": "string",
"Nucleotide GTR": 0,
"MG94xREV with separate rates for branch sets": 0,
"General descriptive": 0,
"k (general descriptive)": 0,
"RELAX null": 0,
"RELAX alternative": 0,
"k (RELAX alternative)": 0,
"tested": true
}
}
}
}
}
}

SLAC

Examples starting jobs and fetching results for SLAC (Single Likelihood Ancestor Counting) analysis

Start a SLAC analysis

SLAC (Single Likelihood Ancestor Counting) uses a maximum likelihood ancestral state reconstruction and minimum path substitution counting to estimate site-level dS and dN, and applies a simple binomial-based test to test if dS differs from dN. The estimates aggregate information over all branches, so the signal is derived from pervasive diversification or conservation.

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
branches	Array of strings Default: [] Branches to include in the analysis. If empty, all branches are included.
samples	integer >= 1 Default: 100 Number of samples for ancestral reconstruction uncertainty
pvalue	number [ 0 .. 1 ] Default: 0.1 Threshold for statistical significance

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"genetic_code": "Universal",
"branches": [ ],
"samples": 100,
"pvalue": 0.1
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a SLAC job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"Nucleotide GTR": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": {"property1": 0,
"property2": 0
},
"display order": 0
},
"Global MG94xREV": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": {"distribution": [[0
]
]
},
"display order": 0
}
},
"branch_attributes": {"property1": {"property1": {"original_name": "string",
"Nucleotide GTR": 0,
"Global MG94xREV": 0,
"codon": [["string"
]
],
"amino_acid": [["string"
]
],
"synonymous_substitution_count": [[0
]
],
"nonsynonymous_substitution_count": [[0
]
]
},
"property2": {"original_name": "string",
"Nucleotide GTR": 0,
"Global MG94xREV": 0,
"codon": [["string"
]
],
"amino_acid": [["string"
]
],
"synonymous_substitution_count": [[0
]
],
"nonsynonymous_substitution_count": [[0
]
]
}
},
"property2": {"property1": {"original_name": "string",
"Nucleotide GTR": 0,
"Global MG94xREV": 0,
"codon": [["string"
]
],
"amino_acid": [["string"
]
],
"synonymous_substitution_count": [[0
]
],
"nonsynonymous_substitution_count": [[0
]
]
},
"property2": {"original_name": "string",
"Nucleotide GTR": 0,
"Global MG94xREV": 0,
"codon": [["string"
]
],
"amino_acid": [["string"
]
],
"synonymous_substitution_count": [[0
]
],
"nonsynonymous_substitution_count": [[0
]
]
}
}
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": [[0
]
],
"property2": [[0
]
]
}
},
"site_results": {"property1": [0
],
"property2": [0
]
}
}
}

Get SLAC analysis results

Retrieve the results of a previously submitted SLAC (Single Likelihood Ancestor Counting) analysis job. Results include model fitting information, branch attributes, and site-specific dN/dS estimates.

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
branches	Array of strings Default: [] Branches to include in the analysis. If empty, all branches are included.
samples	integer >= 1 Default: 100 Number of samples for ancestral reconstruction uncertainty
pvalue	number [ 0 .. 1 ] Default: 0.1 Threshold for statistical significance

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"genetic_code": "Universal",
"branches": [ ],
"samples": 100,
"pvalue": 0.1
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"Nucleotide GTR": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": {"property1": 0,
"property2": 0
},
"display order": 0
},
"Global MG94xREV": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": {"distribution": [[0
]
]
},
"display order": 0
}
},
"branch_attributes": {"property1": {"property1": {"original_name": "string",
"Nucleotide GTR": 0,
"Global MG94xREV": 0,
"codon": [["string"
]
],
"amino_acid": [["string"
]
],
"synonymous_substitution_count": [[0
]
],
"nonsynonymous_substitution_count": [[0
]
]
},
"property2": {"original_name": "string",
"Nucleotide GTR": 0,
"Global MG94xREV": 0,
"codon": [["string"
]
],
"amino_acid": [["string"
]
],
"synonymous_substitution_count": [[0
]
],
"nonsynonymous_substitution_count": [[0
]
]
}
},
"property2": {"property1": {"original_name": "string",
"Nucleotide GTR": 0,
"Global MG94xREV": 0,
"codon": [["string"
]
],
"amino_acid": [["string"
]
],
"synonymous_substitution_count": [[0
]
],
"nonsynonymous_substitution_count": [[0
]
]
},
"property2": {"original_name": "string",
"Nucleotide GTR": 0,
"Global MG94xREV": 0,
"codon": [["string"
]
],
"amino_acid": [["string"
]
],
"synonymous_substitution_count": [[0
]
],
"nonsynonymous_substitution_count": [[0
]
]
}
}
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": [[0
]
],
"property2": [[0
]
]
}
},
"site_results": {"property1": [0
],
"property2": [0
]
}
}
}

NRM

Examples starting jobs and fetching results for NRM (Nucleotide Non-Reversible Model) analysis

Start and monitor an NRM (Nucleotide Non-Reversible Model) job

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
save_fit	boolean Default: false Save NRM+F model fit to a file

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"genetic_code": "Universal",
"save_fit": false
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get an NRM job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": true,
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": [[0
]
],
"display order": 0,
"estimated parameters": 0,
"Equilibrium frequencies": [[0
]
]
},
"property2": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": [[0
]
],
"display order": 0,
"estimated parameters": 0,
"Equilibrium frequencies": [[0
]
]
}
},
"branch attributes": {"property1": {"property1": {"GTR": 0,
"NREV6": 0,
"NREV12": 0,
"NREV12+F": 0,
"observed frequencies": [0
],
"original name": "string"
},
"property2": {"GTR": 0,
"NREV6": 0,
"NREV12": 0,
"NREV12+F": 0,
"observed frequencies": [0
],
"original name": "string"
}
},
"property2": {"property1": {"GTR": 0,
"NREV6": 0,
"NREV12": 0,
"NREV12+F": 0,
"observed frequencies": [0
],
"original name": "string"
},
"property2": {"GTR": 0,
"NREV6": 0,
"NREV12": 0,
"NREV12+F": 0,
"observed frequencies": [0
],
"original name": "string"
}
}
},
"test results": {"property1": {"LRT": 0,
"p-value": 0,
"Corrected P-value": 0
},
"property2": {"LRT": 0,
"p-value": 0,
"Corrected P-value": 0
}
},
"characters": [["string"
]
]
}
}

Get an NRM job result

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
genetic_code	string (GeneticCode) Default: "Universal" Enum: "Universal" "Vertebrate mtDNA" "Yeast mtDNA" "Mold/Protozoan mtDNA" "Invertebrate mtDNA" "Ciliate Nuclear" "Echinoderm mtDNA" "Eupltoid Nuclear" "Alt. Yeast Nuclear" "Ascidian mtDNA" "Flatworm mtDNA" "Blepharisma Nuclear" Available Genetic Codes
save_fit	boolean Default: false Save NRM+F model fit to a file

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"genetic_code": "Universal",
"save_fit": false
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": true,
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": [[0
]
],
"display order": 0,
"estimated parameters": 0,
"Equilibrium frequencies": [[0
]
]
},
"property2": {"AIC-c": 0,
"Log Likelihood": 0,
"Rate Distributions": [[0
]
],
"display order": 0,
"estimated parameters": 0,
"Equilibrium frequencies": [[0
]
]
}
},
"branch attributes": {"property1": {"property1": {"GTR": 0,
"NREV6": 0,
"NREV12": 0,
"NREV12+F": 0,
"observed frequencies": [0
],
"original name": "string"
},
"property2": {"GTR": 0,
"NREV6": 0,
"NREV12": 0,
"NREV12+F": 0,
"observed frequencies": [0
],
"original name": "string"
}
},
"property2": {"property1": {"GTR": 0,
"NREV6": 0,
"NREV12": 0,
"NREV12+F": 0,
"observed frequencies": [0
],
"original name": "string"
},
"property2": {"GTR": 0,
"NREV6": 0,
"NREV12": 0,
"NREV12+F": 0,
"observed frequencies": [0
],
"original name": "string"
}
}
},
"test results": {"property1": {"LRT": 0,
"p-value": 0,
"Corrected P-value": 0
},
"property2": {"LRT": 0,
"p-value": 0,
"Corrected P-value": 0
}
},
"characters": [["string"
]
]
}
}

FADE

Examples starting jobs and fetching results for FADE (FUBAR Approach to Directional Evolution) analysis

Start a FADE job

Start a FADE (FUBAR Approach to Directional Evolution) job. FADE is a fast method to test whether or not a subset of sites in a protein alignment evolve towards a particular residue along a subset of branches at accelerated rates compared to reference model. FADE uses a random effects model and latent Dirichlet allocation (LDA) - inspired approximation methods to allocate sites to rate classes.

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
bayes_factor_threshold	integer [ 1 .. 1000 ] Default: 100 Bayes Factor threshold for determining significant sites (default 100)

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"bayes_factor_threshold": 100
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a FADE job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": { },
"display order": 0
},
"property2": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": { },
"display order": 0
}
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": {"property1": [[0
]
],
"property2": [[0
]
]
},
"property2": {"property1": [[0
]
],
"property2": [[0
]
]
}
}
},
"site annotations": {"headers": {"Composition": "string",
"Substitutions": "string"
},
"site annotations": {"property1": [["string"
]
],
"property2": [["string"
]
]
}
}
}
}

Get a FADE job result

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
alignment	string (Hash) ^[a-zA-Z0-9]+$
tree	string (Hash) ^[a-zA-Z0-9]+$
bayes_factor_threshold	integer [ 1 .. 1000 ] Default: 100 Bayes Factor threshold for determining significant sites (default 100)

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"alignment": "string",
"tree": "string",
"bayes_factor_threshold": 100
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"fits": {"property1": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": { },
"display order": 0
},
"property2": {"Log Likelihood": 0,
"estimated parameters": 0,
"AIC-c": 0,
"Equilibrium frequencies": [[0
]
],
"Rate Distributions": { },
"display order": 0
}
},
"MLE": {"headers": [["string"
]
],
"content": {"property1": {"property1": [[0
]
],
"property2": [[0
]
]
},
"property2": {"property1": [[0
]
],
"property2": [[0
]
]
}
}
},
"site annotations": {"headers": {"Composition": "string",
"Substitutions": "string"
},
"site annotations": {"property1": [["string"
]
],
"property2": [["string"
]
]
}
}
}
}

SLATKIN

Examples starting jobs and fetching results for SLATKIN (Slatkin-Maddison) analysis

Start a Slatkin-Maddison analysis

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

required

string

Token identifying the user

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
tree	string (Hash) ^[a-zA-Z0-9]+$
groups	integer [ 2 .. 100 ] Default: 2 The number of compartments/groups to test
	Array of objects Array of compartment definitions
replicates	integer [ 1 .. 1000000 ] Default: 1000 The number of bootstrap replicates
weight	number [ 0 .. 1 ] Default: 0.2 Probability of branch selection for structured permutation [0-1]; 0 = classical Slatkin-Maddison, 1 = fully structured
use_bootstrap	boolean Default: true Whether to use bootstrap weights to respect well-supported clades

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"tree": "string",
"groups": 2,
"compartment_definitions": [{"description": "string",
"regexp": "string"
}
],
"replicates": 1000,
"weight": 0.2,
"use_bootstrap": true
}

Response samples

200
401
422
500

Content type

application/json

{"job_id": "string",
"alignment_id": "string",
"tree_id": "string",
"status": "queued",
"error_message": "string",
"method": "string"
}

Get a Slatkin-Maddison job result by job ID

query Parameters

pretty_print	boolean Pretty print response
job_id required	string (Hash) ^[a-zA-Z0-9]+$ Job ID to fetch results for

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Responses

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"compartments": 0,
"events": {"property1": {"from": "string",
"to": "string"
},
"property2": {"from": "string",
"to": "string"
}
},
"leaf-count": 0,
"migrations": 0,
"p-value": {"panmictic": 0,
"structured": 0
},
"partition-counts": {"property1": 0,
"property2": 0
},
"partitions": {"property1": {"property1": "string",
"property2": "string"
},
"property2": {"property1": "string",
"property2": "string"
}
},
"replicates": 0,
"node-migrations": {"property1": 0,
"property2": 0
},
"structured-cutoff": 0,
"node-p-value": {"panmictic": {"property1": 0,
"property2": 0
},
"structured": {"property1": 0,
"property2": 0
}
},
"simulations": {"panmictic": [[0
]
],
"structured": [[0
]
]
}
}
}

Get a Slatkin-Maddison job result

query Parameters

pretty_print

boolean

Pretty print response

header Parameters

user_token

string

Token identifying the user (required for private jobs)

Request Body schema: application/json
required

user_token	string Token identifying the user who is starting the job
tree	string (Hash) ^[a-zA-Z0-9]+$
groups	integer [ 2 .. 100 ] Default: 2 The number of compartments/groups to test
	Array of objects Array of compartment definitions
replicates	integer [ 1 .. 1000000 ] Default: 1000 The number of bootstrap replicates
weight	number [ 0 .. 1 ] Default: 0.2 Probability of branch selection for structured permutation [0-1]; 0 = classical Slatkin-Maddison, 1 = fully structured
use_bootstrap	boolean Default: true Whether to use bootstrap weights to respect well-supported clades

Responses

Request samples

Payload

Content type

application/json

{"user_token": "string",
"tree": "string",
"groups": 2,
"compartment_definitions": [{"description": "string",
"regexp": "string"
}
],
"replicates": 1000,
"weight": 0.2,
"use_bootstrap": true
}

Response samples

200
401
403
404
500

Content type

application/json

{"job_id": "string",
"result": {"analysis": {"authors": null,
"citation": null,
"contact": "john.smith@example.com",
"info": null,
"requirements": null,
"settings": {"ci": null,
"multihit": null,
"pvalue": null,
"resample": null,
"site_filter": {"site_filter": null,
"site_save_filter": null
},
"srv": null
},
"version": null
},
"input": {"file_name": null,
"number_of_sequences": null,
"number_of_sites": null,
"partition_count": null,
"trees": {"property1": "string",
"property2": "string"
}
},
"tested": {"property1": {"property1": "tested",
"property2": "tested"
},
"property2": {"property1": "tested",
"property2": "tested"
}
},
"timers": {"property1": {"order": 0,
"timer": 0
},
"property2": {"order": 0,
"timer": 0
}
},
"runtime": "string",
"data partitions": {"property1": {"name": "string",
"coverage": [[0
]
]
},
"property2": {"name": "string",
"coverage": [[0
]
]
}
},
"compartments": 0,
"events": {"property1": {"from": "string",
"to": "string"
},
"property2": {"from": "string",
"to": "string"
}
},
"leaf-count": 0,
"migrations": 0,
"p-value": {"panmictic": 0,
"structured": 0
},
"partition-counts": {"property1": 0,
"property2": 0
},
"partitions": {"property1": {"property1": "string",
"property2": "string"
},
"property2": {"property1": "string",
"property2": "string"
}
},
"replicates": 0,
"node-migrations": {"property1": 0,
"property2": 0
},
"structured-cutoff": 0,
"node-p-value": {"panmictic": {"property1": 0,
"property2": 0
},
"structured": {"property1": 0,
"property2": 0
}
},
"simulations": {"panmictic": [[0
]
],
"structured": [[0
]
]
}
}
}

Codon Aware Alignments

Examples building codon-aware alignments from uploaded data. Somewhere over the rainbow..

Tree Building

Examples building phylogenetic trees from uploaded data. Somewhere over the rainbow..

Datamonkey API (1.2.0)

Health

Check health of Datamonkey

query Parameters

Responses

Response samples

Chat

List conversations for the authenticated user

header Parameters

Responses

Response samples

Create a new conversation

header Parameters

Request Body schema: application/jsonoptional

Responses

Request samples

Response samples

Get a conversation by ID

path Parameters

header Parameters

Responses

Response samples

Delete a conversation

path Parameters

header Parameters

Responses

Response samples

Get messages from a conversation

path Parameters

header Parameters

Responses

Response samples

Send a message to the conversation

path Parameters

header Parameters

Request Body schema: application/jsonrequired

Responses

Request samples

Response samples

File Upload and QC

Get a list of datasets uploaded to Datamonkey

query Parameters

Responses

Response samples

Upload a dataset to Datamonkey

query Parameters

header Parameters

Request Body schema: multipart/form-datarequired

Responses

Response samples

Get details for a specific dataset

path Parameters

query Parameters

header Parameters

Responses

Response samples

Delete a dataset

path Parameters

query Parameters

header Parameters

Responses

Response samples

Jobs

Get a list of jobs

query Parameters

Responses

Response samples

Get details for a specific job

path Parameters

query Parameters

header Parameters

Responses

Response samples

Delete a job

path Parameters

query Parameters

header Parameters

Responses

Response samples

Methods

Request Body schema: application/json
optional

Request Body schema: application/json
required

Request Body schema: multipart/form-data
required

Request Body schema: application/json
required

Request Body schema: application/json
required

Request Body schema: application/json
required

Request Body schema: application/json
required

Request Body schema: application/json
required

Request Body schema: application/json
required

Request Body schema: application/json
required