What does POPTREEW do?

POPTREEW constructs phylogenetic trees from allele frequency data by using the neighbor-joining method (Saitou and Nei 1987) and the unweighted pair-group method with arithmetic mean (UPGMA) (Sneath and Sokal 1973). Bootstrap test can be performed for phylogenetic trees. POPTREEW also computes heterozygosities and GST, the measures of the extent of genetic variation in a population and genetic differentiation among subdivided populations.

Distance measures that can be used for the phylogeny construction are as follows:

  1. DA distance (Nei et al. 1983)
  2. Nei's standard genetic distance (DST) (Nei 1972)
  3. FST* distance (Latter 1972)
  4. (δμ)2 distance (Goldstein et al. 1995)
  5. DSW distance (Shriver et al. 1995)
(δμ)2 distance and DSW distance can be used only for microsatellite DNA data, in which alleles are represented by the number of repeats. By contrast, DA, DST, and FST* can be used for any kind of allele frequency data. DST and FST* are computed by the original method without sample size bias correction as well as with the bias correction (Nei 1978, 1987).

Quantities that POPTREEW can compute in addition to construction of the phylogenetic trees are as follows:

  1. Average heterozygosities (H) and its standard error for each population
  2. Number of alleles for each population
  3. Measures of genetic differentiation among subdivided populations and their standard errors
  4. Values of distance measures 1-5
Heterozygosities and GST, standardized GST, and Jost's D are computed without sample size bias correction (Nei 1973) or with bias correction (Nei and Roychoudhury 1974, Nei 1987).


The web-interface of POPTREEW has an intuituve and simple design, as the Windows-interface of POPTREE2. All the results of the analyses can be obtained by clicking icons and choosing options under pull-down menus. The displayed tree can be printed and changed interactively using icons on the window. The image file in EMF format or the tree file in Newick format can be downloaded.


About authors

Koichiro Tamura is Professor of Tokyo Metropolitan University, and a primary author of MEGA 6 (Molecular Evolutionary Genetics Analysis), software for evolutionary analyses of DNA and protein sequences.

Masatoshi Nei is Evan Pugh Professor of the Department of Biology at Pennsylvania State University and Director of the Institute of Molecular Evolutionary Genetics.

Naoko Takezaki
Life Science Research Center, Kagawa University
Ikenobe 1750-1, Mikicho, Kitagun, Kagawa 760-0793
takezaki at med.kagawa-u.ac.jp
December 26, 2013

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