Convert a FASTA alignment to SNP distance matrix
% cat test/good.aln
>seq1
AGTCAGTC
>seq2
AGGCAGTC
>seq3
AGTGAGTA
>seq4
TGTTAGAC
% snp-dists test/good.aln > distances.tab
Read 4 sequences of length 8
% cat distances.tab
snp-dists 0.2 seq1 seq2 seq3 seq4
seq1 0 1 2 3
seq2 1 0 3 4
seq3 2 3 0 4
seq4 3 4 4 0
brew tap tseemann/bioinformatics-linux
brew install snp-dists
snp-dists is written in C to the C99 standard and only depends on libz.
Ensure you have a standard development environment installed (e.g. gcc, automake, autoconf, libtool).
git clone https://github.com/tseemann/snp-dists.git
cd snp-dists
autoreconf -i -f
./configure
make
sudo make install
Install Docker. To build the container from scratch:
git clone https://github.com/tseemann/snp-dists.git
cd snp-dists
docker build .
Alternatively you can pull in a prebuilt container from docker hub.
docker pull tseemann/snpdists
To use it you would use a command such as this (substituting in your
directories), where your files are assumed to be stored in
/home/ubuntu/data:
docker run --rm -it -v /home/ubuntu/data:/data tseemann/snpdists tseemann/snpdists
To install on a modern Debian or Ubuntu based system, run the commands below as root:
apt-get update -qq && apt-get install -y build-essential git zlib1g-dev automake autoconf libtool check pkg-config
git clone https://github.com/tseemann/snp-dists.git
cd snp-dists && autoreconf -i -f && ./configure && make && make install
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
To install on a modern RHEL or Centos based system, run the commands below as root:
yum groupinstall 'Development Tools'
yum install git check
git clone https://github.com/tseemann/snp-dists.git
cd snp-dists && autoreconf -i -f && ./configure && make && make install
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
SYNOPSIS
Pairwise SNP distance matrix from a FASTA alignment
USAGE
snp-dists [options] alignment.fasta > matrix.tsv
OPTIONS
-h Show this help
-v Print version and exit
-q Quiet mode; do not print progress information
-c Output CSV instead of TSV
-b Blank top left corner cell instead of 'snp-dists 0.2'
URL
https://github.com/tseemann/snp-dists
Prints the name and version separated by a space in standard Unix fashion.
snp-dists 0.2
Don't print informational messages, only errors.
snp-dists 0.2,seq1,seq2,seq3,seq4
seq1,0,1,2,3
seq2,1,0,3,4
seq3,2,3,0,4
seq4,3,4,4,0
seq1 seq2 seq3 seq4
seq1 0 1 2 3
seq2 1 0 3 4
seq3 2 3 0 4
seq4 3 4 4 0
File problems here: https://github.com/tseemann/snp-dists/issues
- Torsten Seemann
- Andrew J Page
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