bioinformaticsarchive / andi

About

This is the andi program for estimating the evolutionary distance between closely related genomes.

Build Instructions

For the latest stable release of andi download the tar ball. If you'd like to contribute to this software, feel free to create a fork of our git repository and send pull requests.

Prerequisites

This program has the following dependencies: kseq.h, RMQ_improved and libdivsufsort. The former two are included in the lib directory. Please make sure you installed the latter 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. Run autoreconf -i to generate the configure script and continue with the next step.

Compiling

Assuming you have installed all prerequisites, building is as easy as follows.

$ ./configure
$ make
$ make install

Excessive build instructions are located in INSTALL. If the build was successful you can get the usage instructions via --help or the man page.

$ andi --help
$ man andi

Code documentation is provided via doxygen.

$ make code-docs

Unit Test

To run the unit tests, you also need to install GLIB2 and enable the unit tests at configuration time as follows.

$ ./configure --enable-unit-tests
$ make check

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.

Data Sets

1. 29. E. coli strains: data
2. 109 E. coli ST131 strains (paper):
   • 99 newly sequenced strains
   • 10 previously published strains
3. 3085 Streptococcus pneumoniae strains (paper): ftp://ftp.sanger.ac.uk/pub/pathogens/Streptococcus/pneumoniae/Maela_assemblies.tgz

License

Copyright © 2014 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.