Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Shell C Python Other

This branch is 565 commits behind sanger-pathogens:master

Fetching latest commit…

Cannot retrieve the latest commit at this time

Failed to load latest commit information.
m4
src
tests
.DS_Store
.gitignore
AUTHORS
ChangeLog
INSTALL
Makefile.am
Makefile.in
README
aclocal.m4
config.guess
config.h
config.h.in
config.log
config.status
config.sub
configure
configure.ac
depcomp
install-sh
libtool
ltmain.sh
missing
run_gubbins.py
stamp-h1

README

This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the snp sites in the following formats:
VCF, 
a multi fasta alignment,
relaxed phylib format.

The first sequence in the input file is taken as the reference.

To use:

multi_fasta_to_vcf my_file.aln


VCF
=====
This contains the position of each SNP in the reference sequence, and the occurance in each other sample.

Multi Fasta Alignment
=====
Similar to the input file but just containing the snpsites.

Relaxed Phylib format
=====
All the snpsites in a format for RAxML


Something went wrong with that request. Please try again.