Alignment & variants

Pairwise identity matrix

Percent identity between every pair in a multiple alignment. Takes ALIGNED sequences — the output of multiple_sequence_alignment — because inferring an alignment here would bury the aligner's parameters inside a number that reads as a property of the sequences. Two percentages come back per pair: over columns where both have a residue (the usual figure), and over all columns including gaps. The gap between them is the warning — two sequences overlapping in 50 of 2,000 columns read 100% by the first measure and 2.5% by the second.

post/identity_matrix

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/identity_matrix
  • Auth: none required

Request body

sequencesstring required

Aligned FASTA (gaps as "-"), or an array of {id, sequence}. All rows must be the same length. Max 200 sequences.

caseSensitiveboolean

Treat upper and lower case as different residues. Off by default — soft-masking is not a mismatch.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.