Awesome
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