Distance Matrix Builder

About

This is a command line tool for making a distance matrix for a set of aligned sequences. The input sequences are in FASTA format, the output matrix is in PHYLIP format.

Download

• distance-matrix-builder-0.2.1.zip - v.0.2.1 source code, 2025-06-17

Distributed under the zlib/libpng license, see the license.txt file for details.

Usage

distance-matrix-builder [OPTIONS] --in alignment.fasta --out matrix.txt
distance-matrix-builder [OPTIONS] <alignment.fasta >matrix.txt

OPTIONS may include:
   --in PATH      - Specify file with input sequences (standard input if omitted)
   --out PATH     - Specify output file name (standard output if omitted)
   --p-distance   - Compute p-distances (default)
   --integer      - Compute integer distances
   --lower-left   - Produce only the lower left half of the matrix
   --square       - Produce a square matrix (default)
   --n-threads N  - Use N threads (cores) (1 by default)
   --verbose      - Verbose mode
   --version      - Print version
   --help         - Print usage help

When executed without parameters, it tries to read sequences from standard input and prints distances to standard output. This is useful for re-directing the data from/to other programs.

Please send any feedback to kkryukov@gmail.com.

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