pANIto

Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment.

Contents

• Introduction
• Installation
  • OSX/Linux - from source
  • OSX/Linux - Homebrew
• Usage
  • Input format
  • Output
• License
• Feedback/Issues
• Etymology

Introduction

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.

Installation

OSX/Linux - from source

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

OSX/Linux - Homebrew

brew tap tseemann/bioinformatics-linux
brew install panito

Usage

   $ 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

Input format

The input file must be a multi-FASTA file, where all sequences are the same length:

   >sample1
   AAAAAAAAAA
   >sample2
   AAAAAAAAAC
   >sample3
   AAAAAAAACC

Output

        sample1     sample2     sample3
sample1 100.000000  90.00000    80.000000
sample2 -           100.000000  90.000000
sample3 -           -           100.000000

License

pANIto is free software, licensed under GPLv3

Feedback/Issues

Please report any issues to the Issues page or email path-help@sanger.ac.uk.

Etymology

pANIto has 'ani' in the middle. In Spanish it means babylon.