This is the
andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because
andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.
This readme covers all necessary instructions for the impatient to get
andi up and running. For extensive instructions please consult the manual.
Installation and Usage
Stable versions of
andi are available via package managers. For manual installation see below.
For Debian and Ubuntu:
sudo apt-get install andi
For OS X with Homebrew:
brew tap brewsci/bio brew install andi
For ArchLinux with aura:
sudo aura -A andi
With a successful installation you can get the usage instructions via
--help or the man page.
$ andi --help $ man andi
You can simply use
andi with your genomes in
$ andi S1.fasta S2.fasta 2 S1 0.0 0.1 s2 0.1 0.0
From this distance matrix the phylogeny can be inferred via neighbor-joining. Check the manual for a more thorough description.
This program has the following external dependencies: libdivsufsort and the GSL. Please make sure you installed both before attempting a build. If you did get the source, not as a tarball, but straight from the git repository, you will also need the autotools.
Assuming you have installed all prerequisites, building is as easy as follows.
$ autoreconf -fi -Im4 # optional when build from tarball $ ./configure $ make $ make install
Excessive build instructions are located in
Links and Additional Resources
The release of this software is accompanied by a paper from Haubold et al.. It explains the used anchor distance strategy in great detail. The
maf2phy.awk script used in the validation process is located under
scripts. Simulations were done using our own simK tool. For a demo visualising the internals of andi visit our GitHub pages.
- 29 E. coli and Shigella strains: data
- 109 E. coli ST131 strains (paper):
- 3085 Streptococcus pneumoniae strains (paper): ftp://ftp.sanger.ac.uk/pub/pathogens/Streptococcus/pneumoniae/Maela_assemblies.tgz
Copyright © 2014 - 2018 Fabian Klötzl
License GPLv3+: GNU GPL version 3 or later.
This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at http://gnu.org/licenses/gpl.html.
Some files may be licensed differently.
In case of bugs or unexpected errors don't hesitate to send me a mail: firstname.lastname@example.org