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LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
2004 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 20, no 3, 416-418 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2004. Vol. 20, no 3, 416-418 p.
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Bioinformatics and Systems Biology
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URN: urn:nbn:se:uu:diva-70314DOI: 10.1093/bioinformatics/btg422OAI: oai:DiVA.org:uu-70314DiVA: diva2:98225
Available from: 2005-04-20 Created: 2005-04-20 Last updated: 2017-11-21Bibliographically approved

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Thollesson, Mikael

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