Benchling · Schema

ClustaloOptions

Options to pass to the ClustalO algorithm, only applicable for ClustalO.

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Properties

Name	Type	Description
maxGuidetreeIterations	integer	Max guide tree iterations within combined iterations. Use -1 for no max (all iterations will include guide tree iterations).
maxHmmIterations	integer	Max HMM iterations within combined iterations. Use -1 for no max (all iterations will include HMM iterations).
mbedGuideTree	boolean	Whether mBed-like clustering guide tree should be used (faster to use it).
mbedIteration	boolean	Whether mBed-like clustering iteration should be used (faster to use it).
numCombinedIterations	integer	Number of (combined guide-tree/HMM) iterations.

View JSON Schema on GitHub

JSON Schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://api-evangelist.github.io/benchling/json-schema/ClustaloOptions.json",
  "title": "ClustaloOptions",
  "description": "Options to pass to the ClustalO algorithm, only applicable for ClustalO.",
  "properties": {
    "maxGuidetreeIterations": {
      "default": -1,
      "description": "Max guide tree iterations within combined iterations. Use -1 for no max (all iterations will include guide tree iterations).",
      "maximum": 5,
      "minimum": -1,
      "type": "integer"
    },
    "maxHmmIterations": {
      "default": -1,
      "description": "Max HMM iterations within combined iterations. Use -1 for no max (all iterations will include HMM iterations).",
      "maximum": 5,
      "minimum": -1,
      "type": "integer"
    },
    "mbedGuideTree": {
      "default": true,
      "description": "Whether mBed-like clustering guide tree should be used (faster to use it).",
      "type": "boolean"
    },
    "mbedIteration": {
      "default": true,
      "description": "Whether mBed-like clustering iteration should be used (faster to use it).",
      "type": "boolean"
    },
    "numCombinedIterations": {
      "default": 0,
      "description": "Number of (combined guide-tree/HMM) iterations.",
      "maximum": 5,
      "minimum": 0,
      "type": "integer"
    }
  },
  "type": "object"
}