necom Documentation

Evaluate clustering partitions and phylogenetic trees.

Input:

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

Notes:

• Subcommand groups:
  • Tree comparison: compare
  • Partition evaluation: partition
  • Branch support: replicate
• Run necom eval <subcommand> --help for command-specific options.
• eval compare reads from stdin if the input file is stdin.
• eval partition accepts stdin for p1 and for --other/--matrix/--tree/--coords.
• eval replicate accepts stdin for the target or replicates file (but not both at once).

Examples:

1. Show available subcommands necom eval --help