PHASE
Description
PHASE is a program for reconstructing haplotypes from population data.
License
The program is available under following open source license: https://github.com/stephens999/phase/blob/master/license.md
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of phase and load default version of phase as
module avail phase/ # list available modules module load phase # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail phase
and choose explicit version you want to use.
Now you can run the program using 'phase <filename.inp> <filename.out> <number of iterations> <thinning interval> <burn-in>'.
Documentation
Official website: http://stephenslab.uchicago.edu/phase/download.html
The documentation itself (in PDF): http://stephenslab.uchicago.edu/assets/software/phase/instruct2.1.pdf
You can also find this PDF in the folder '/software/phase/2.1.1/doc'.