LDDist
Description
LDDist is a Perl module implemente in C++ that enables the user to calculate LogDet pair-wise genetic distances based on amino acid as well as DNA/RNA sequences. Site-to-site rate heterogeneity is handled by excluding invariant sites and/or bu assigning sites to different rate classes that are treated separately.
License
PAL (Perl Artistic License)
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 lddist and load default version of lddist as
module avail lddist/ # list available modules module load lddist # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail lddist
and choose explicit version you want to use. Then run "PLD.pl".
Documentation
Documentation is available on WWW server.