necom Documentation

Compare two PHYLIP distance matrices and calculate similarity metrics.

Input:

• Two PHYLIP distance matrices (full or lower-triangular).
• Only the intersection of common IDs is used for comparison.

Output:

• Tab-separated values with two columns: Method and Score.
• One row per requested method.

Notes:

• Available methods:
  • all: calculate all metrics below.
  • pearson: Pearson correlation coefficient (-1 to 1).
  • spearman: Spearman rank correlation (-1 to 1).
  • mae: mean absolute error.
  • cosine: cosine similarity (-1 to 1).
  • jaccard: weighted Jaccard similarity (0 to 1).
  • euclid: Euclidean distance.
• Useful for evaluating consistency between distance calculation methods, or measuring information loss before and after clustering (Cophenetic Correlation).
• Default method is pearson.
• Multiple methods can be requested as a comma-separated list.
• Non-finite scores (NaN / Inf) are emitted as NA to keep the TSV parseable.

Examples:

1. Compare using Pearson correlation necom mat compare matrix1.phy matrix2.phy --method pearson

2. Compare using multiple methods necom mat compare matrix1.phy matrix2.phy --method pearson,cosine,jaccard