necom Documentation

Convert pairwise distances to a PHYLIP distance matrix.

Input:

• Tab-separated values (TSV).
• Three columns: name1, name2, distance.

Output:

• A full PHYLIP distance matrix.
• All observed IDs are collected and arranged into a square matrix.

Notes:

• Typical input comes from alignment results (e.g., blast --outfmt 6).
• Use --same to set the distance for self-to-self pairs (diagonal), default 0.0.
• Use --missing to set the distance for pairs without input records, default 1.0.
• The default missing value represents maximum distance, which is useful for unaligned sequences.

Examples:

1. Convert pairwise distances to a PHYLIP matrix necom mat to-phylip input.tsv -o output.phy