♥ Fast and Accurate Estimation of Evolutionary Distances
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Readme.md

Phylonium - fast and accurate estimation of evolutionary distances

This is the phylonium program for estimating the evolutionary distances between closely related genomes. It is much faster than alignment based approaches for phylogeny reconstruction and usually more accurate than competing alignment-free methods.

Dependencies, Installation and Usage

This program depends on two external libraries: libdivsufsort and the GSL. Both should be available for installation through a package manager of your choice. Furthermore, to build from the git repository the autotools are required.

Assuming all prerequisites are installed, the build can be started as follows.

$ autoreconf -fi -Im4
$ ./configure
$ make
$ make install

After a successful build the phylonium executable is found in the src directory. It can then be run as a simple command line tool. All the sequences in one FASTA file are considered to be contigs of the same genome. The filename without the extension is used as ID in the output.

$ phylonium Seq1.fasta Seq2.fasta
2
Seq1     0.0  0.1
Seq2     0.1  0.0

The output is a distance matrix in PHYLIP format. Use phylip neighbor, mat nj from mattools or any other neighbor-joining implementation to build the phylogenetic tree.

License

Copyright © 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.

Individual files may be licensed differently.

Contact

In case of bugs or unexpected errors don't hesitate to send me a mail: kloetzl@evolbio.mpg.de