Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment.
Given a multi-FASTA alignment, output the genome wide average nucleotide identity (gwANI) for each sample against all other samples. A matrix containing the percentages is outputted. This software loads the whole file into memory.
Ensure you have a standard development environment installed (e.g. gcc, automake, autoconf, libtool). Download the software from GitHub and unzip.
autoreconf -i -f
./configure
make
sudo make install
brew tap tseemann/bioinformatics-linux
brew install panito
$ panito
Usage: panito [-hV] <file>
This program calculates the genome wide ANI for a multiFASTA alignment.
-h this help message
-V print version and exit
<file> input alignment file which can optionally be gzipped
The input file must be a multi-FASTA file, where all sequences are the same length:
>sample1
AAAAAAAAAA
>sample2
AAAAAAAAAC
>sample3
AAAAAAAACC
sample1 sample2 sample3
sample1 100.000000 90.00000 80.000000
sample2 - 100.000000 90.000000
sample3 - - 100.000000
pANIto is free software, licensed under GPLv3
Please report any issues to the Issues page or email path-help@sanger.ac.uk.
pANIto has 'ani' in the middle. In Spanish it means babylon.