| 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. PLD.pl is a companion script that serves as a front-end and example of how to use LDDist. |
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| Language | C++ and Perl | |
| Target OS/HW | Any platform with a Perl distribution and a C++ compiler. Tested on Linux and Mac OS X. | |
| Requirements | PLD.pl requires BioPerl::AlignIO and GetOpt::Std | |
| Author | Mikael Thollesson, Molecular Evolution, Evolutionary Biology Centre, Uppsala University | |
| Contact | lddist@artedi.ebc.uu.se | |
| License | LDDist and companion code is released under the terms of the Perl Artistic License, http://www.perl.com/pub/language/misc/Artistic.html | |
| Citation | LDDist has been reported as an Application note in Bioinformatics (Thollesson, M. 2004. LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences. Bioinformatics 20:416-418). If you publish anything using LDDist, that paper together with the relase number is the suggested citation. | |
| History |
1.3.2 Released 2005-06-28. Minor update to acommodate changes in C++ standard. No new features. 1.3 Released 2003-12-10. PLD is updated to read more alignment file formats, and there is a different implementation of the determinant calculation in LDDist. 1.1 Released 2003-03-03. LDDist now handles DNA seqeuences in addition to amino acid sequences and capture-recapture estimation of invariant sites according to Steel et al. 1.0 Released 2002-11-19. First publicly available version. |
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| Installation |
Download and uncompress the distribution file (e.g., tar xvfz LDDist1.3). Then, in the extracted directory, run (the last as root)
to install the LDDist.pm module. The companion/example script PLD.pl can be placed and run in any directory. |
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| Download | http://artedi.ebc.uu.se/molev/software/LDDist-1.3.2.tar.gz | |
| Documentation | Work in progress… Some documentaion as POD in LDDist.pm |
| The usual disclaimer This software is provided "as is" without warranty of any kind. The author(s) and Uppsala University do not warrant, guarantee, or make any representations regarding the use or the results of the software or documentation in terms of their correctness, reliability, currentness, or otherwise. In no case will these parties be liable for any special, incidental, consequential, or other damages that may result from the use of this software. |
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| This page was last updated: 2005-09-05 09:19:23 |