POPTREEW: web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities

Naoko Takezaki; Masatoshi Nei; Koichiro Tamura

doi:10.1093/molbev/msu093

POPTREEW: web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities

Mol Biol Evol. 2014 Jun;31(6):1622-4. doi: 10.1093/molbev/msu093. Epub 2014 Mar 6.

Authors

Naoko Takezaki¹, Masatoshi Nei², Koichiro Tamura³

Affiliations

¹ Life Science Research Center, Kagawa University, Kagawa, Japan takezaki@med.kagawa-u.ac.jp.
² Department of Biology and the Institute of Molecular Evolutionary Genetics, the Pennsylvania State University.
³ Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.

PMID: 24603277
DOI: 10.1093/molbev/msu093

Abstract

POPTREE software, including the command line (POPTREE) and the Windows (POPTREE2) versions, is available to perform evolutionary analyses of allele frequency data, computing distance measures for constructing population trees and average heterozygosity (H) (measure of genetic diversity within populations) and G(ST) (measure of genetic differentiation among subdivided populations). We have now developed a web version POPTREEW (http://www.med.kagawa-u.ac.jp/∼genomelb/takezaki/poptreew/) to provide cross-platform access to all POPTREE functions including interactive tree editing. Furthermore, new POPTREE software (POPTREE, POPTREE2, and POPTREEW) computes standardized G(ST) and Jost's D, which may be appropriate for data with high variability, and accepts genotype data in GENEPOP format as an input.

Keywords: allele frequency data; genetic differentiation; genetic diversity; microsatellite DNA; population tree; web interface.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biological Evolution
Gene Frequency*
Genetic Drift
Genetic Variation
Genetics, Population
Internet
Models, Genetic
Phylogeny
Software*