necom Documentation

Operate on distance matrices.

Input:

• mat is a command group; use one of its subcommands directly.

Notes:

• Subcommands:
  • compare: compare two PHYLIP distance matrices.
  • format: convert between PHYLIP matrix variants.
  • from-vector: calculate pairwise similarity/distance from vector inputs.
  • subset: extract a submatrix using a name list.
  • to-pair: flatten a PHYLIP matrix to pairwise TSV.
  • to-phylip: assemble pairwise TSV into a PHYLIP matrix.
  • transform: apply mathematical transformations to matrix elements.
• Run necom mat <subcommand> --help for command-specific options.
• Reads from stdin if input file is ‘stdin’.

Examples:

1. Show available subcommands necom mat --help