Bioinformatics Advance Access originally published online on January 22, 2004
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Bioinformatics 20(3) © Oxford University Press 2004; all rights reserved.
Applications Note |
LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences
Department of Molecular Evolution, Evolutionary Biology Centre and Linnaeus Centre for Bioinformatics, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
Received on April 25, 2003
; revised on July 29, 2003
; accepted on August 8, 2003
Advance Access Publication January 22, 2004
Summary: LDDist is a Perl module implemented in C++ that allows the user to calculate LogDet pair-wise genetic distances for amino acid as well as nucleotide sequence data. It can handle site-to-site rate variation by treating a proportion of the sites as invariant and/or by assigning sites to different, presumably homogenous, rate categories. The rate-class assignments and invariant proportion can be set explicitly, or estimated by the program; the latter using either of two different capture–recapture methods. The assignment to rate categories in lieu of a phylogeny can be done using Shannon–Wiener index as a crude token for relative rate.
Availability: LDDist and its companion Perl script PLD are freely available at http://artedi.ebc.uu.se/molev/software/LDDist.html
Contact: lddist{at}artedi.ebc.uu.se
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