necom Documentation

Convert a PHYLIP matrix between formats.

Input:

• PHYLIP distance matrix (full or lower-triangular).
• Optional first line: number of sequences.
• Each line: sequence name followed by distances.

Output:

• full (default):
  • Full square matrix.
  • Tab-separated values.
  • Original sequence names preserved.
• lower:
  • Lower triangular matrix without diagonal values.
  • Tab-separated values.
  • Original sequence names preserved.
  • Row i contains i tab-separated values.
  • Useful for saving disk space.
• strict:
  • Standard PHYLIP format.
  • Names truncated to 10 bytes.
  • Names left-aligned with space padding.
  • Distances formatted to 6 decimal places, space-separated.
  • Space-separated values.
  • Use this for compatibility with the original PHYLIP toolkit.

Notes:

• strict mode truncates names to 10 bytes and formats distances to 6 decimal places, which can cause name collisions and precision loss.
• full and lower preserve original names without truncation.
• full and lower preserve distance values as-is; strict may round them to 6 decimal places.

Examples:

1. Create a full matrix necom mat format input.phy -o output.phy

2. Create a lower-triangular matrix necom mat format input.phy --format lower -o output.phy

3. Create a strict PHYLIP matrix necom mat format input.phy --format strict -o output.phy