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Disty McMatrixface - compute a distance matrix from a core genome alignment file
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readme.md

Disty McMatrixface

Compute a distance matrix from a core genome alignment file.

Prerequisities

  • GCC 4.8+ or equivalent
  • ZLib

Getting started

git clone https://github.com/c2-d2/disty
cd disty && make
./disty tests/test2.fa

Output:

	seq1	seq2	seq3
seq1	0	3	1
seq2	3	0	1
seq3	1	1	0

Installation

Using Bioconda:

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

conda install disty

Using brew:

brew install tseemann/bioinformatics-linux/disty

From Github:

git clone https://github.com/c2-d2/disty
cd disty && make && make install

Command line parameters

Usage:   disty <alignment.fa>

Options:
  -n  FLOAT  skip columns having frequency of N > FLOAT [1.00]
  -i  INT    input format [0]
                 0: ACGT
                 1: 01
  -s  INT    strategy to deal with N's [0]
                 0: ignore pairwisely
                 1: ignore pairwisely and normalize
                 2: ignore globally
                 3: replace by the major allele
                 4: replace by the closest individual (not implemented yet)
  -h         print help message and exit
  -v         print version and exit

Author

Karel Brinda <kbrinda@hsph.harvard.edu>

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