Benchling · Schema

MafftOptions

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

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Properties

Name	Type	Description
adjustDirection	string	Adjust direction: * `fast`: Enabled, quickly. * `accurate`: Enabled, accurately (slow). * `disabled`: Disabled, fastest.
gapExtensionPenalty	number	Gap extension penalty.
gapOpenPenalty	number	Gap open penalty.
maxIterations	integer	Max refinement iterations. Not applicable for auto strategy, as it will be selected automatically.
retree	integer	Tree rebuilding. Only used for 6-mer strategy.
strategy	string	MAFFT Strategy: * `auto`: Pick a strategy automatically based on the count and size of inputs. * `sixmer`: Use 6-mer distance for constructing the guide tree. * `localpair`: Compute local pairwise ali

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/MafftOptions.json",
  "title": "MafftOptions",
  "description": "Options to pass to the MAFFT algorithm, only applicable for MAFFT.",
  "properties": {
    "adjustDirection": {
      "default": "fast",
      "description": "Adjust direction:\n  * `fast`: Enabled, quickly.\n  * `accurate`: Enabled, accurately (slow).\n  * `disabled`: Disabled, fastest.\n",
      "enum": [
        "fast",
        "accurate",
        "disabled"
      ],
      "type": "string"
    },
    "gapExtensionPenalty": {
      "default": 0.0,
      "description": "Gap extension penalty.",
      "type": "number"
    },
    "gapOpenPenalty": {
      "default": 1.53,
      "description": "Gap open penalty.",
      "type": "number"
    },
    "maxIterations": {
      "default": 0,
      "description": "Max refinement iterations. Not applicable for auto strategy, as it will be selected automatically.",
      "type": "integer"
    },
    "retree": {
      "default": 2,
      "description": "Tree rebuilding. Only used for 6-mer strategy.",
      "type": "integer"
    },
    "strategy": {
      "default": "auto",
      "description": "MAFFT Strategy:\n  * `auto`: Pick a strategy automatically based on the count and size of inputs.\n  * `sixmer`: Use 6-mer distance for constructing the guide tree.\n  * `localpair`: Compute local pairwise alignments using Smith-Waterman for constructing the guide tree and iterative refinement.\n  * `globalpair`: Compute global pairwise alignments using Needleman-Wunsch for constructing the guide tree and iterative refinement.\n",
      "enum": [
        "auto",
        "sixmer",
        "localpair",
        "globalpair"
      ],
      "type": "string"
    }
  },
  "type": "object"
}