POPTREEW statistics

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Citations per year

Number of citations per year for the bioinformatics software tool POPTREEW
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Tool usage distribution map

This map represents all the scientific publications referring to POPTREEW per scientific context
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Associated diseases

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Protocols

POPTREEW specifications

Information


Unique identifier OMICS_13051
Name POPTREEW
Alternative name POPTREE
Interface Web user interface
Restrictions to use None
Input data Allele frequency data, genotype data
Input format DAT, GENEPOP
Output data Phylogenetic tree, distance matrix, heterozygosities
Output format NEWICK
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Naoko Takezaki

Information


Unique identifier OMICS_13051
Name POPTREEW
Alternative name POPTREE
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Allele frequency data, genotype data
Input format DAT, GENEPOP
Output data Phylogenetic tree, distance matrix, heterozygosities
Output format NEWICK
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Naoko Takezaki

Publication for POPTREEW

POPTREEW citations

 (27)
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Single nucleotide polymorphisms in native South American Atlantic coast populations of smooth shelled mussels: hybridization with invasive European Mytilus galloprovincialis

2018
PMCID: 5824471
PMID: 29471805
DOI: 10.1186/s12711-018-0376-z
call_split See protocol

[…] tions was determined based on allele frequencies of SNPs using pairwise FST values in Arlequin. The FST distance measures in the Newick format, which were obtained from SNP allele frequencies data in POPTREEW [] were used to construct a neighbour-joining (NJ) tree with the MEGA software version 6 []. Robustness of relationships was assessed using 10,000 bootstrap replicates. We used two methods fo […]

library_books

The origin of multiple clones in the parthenogenetic lizard species Darevskia rostombekowi

2017
PLoS One
PMCID: 5607197
PMID: 28931071
DOI: 10.1371/journal.pone.0185161

[…] unts adjusted for sample size, and expected heterozygosity, as a measure of gene diversity, were calculated per locus and per population by using Fstat v.2.9.3.2 [], GenePop v.4.2, and Web-version of POPTREEW []. Analysis of molecular variance AMOVA was carried out using the package poppr []. We implemented multiple alignments of microsatellite allele sequences obtained from the three species by u […]

library_books

Development and Application of Transcriptome Derived Microsatellites in Actinidia eriantha (Actinidiaceae)

2017
Front Plant Sci
PMCID: 5574902
PMID: 28890721
DOI: 10.3389/fpls.2017.01383

[…] r, ) with 10,000 permutations. Neighbor-joining (NJ) networks revealing the genetic relationships among populations were generated based on DA distances (Takezaki and Nei, ) between populations using POPTREE (version 2; Takezaki et al., ). Bootstrap values were calculated from 100,000 replicates of resampled loci. Finally, a Bayesian clustering approach was used to assign individuals to genetic cl […]

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Population structure of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) in Asia

2017
PLoS One
PMCID: 5489206
PMID: 28658282
DOI: 10.1371/journal.pone.0180000
call_split See protocol

[…] 3 []. Population bottleneck was estimated based on 1000 replications using BOTTLENECK software []. A phylogenetic tree was constructed based on genetic distance matrices from allele frequencies using POPTREE with 1000 bootstrap replications [].AMOVA was conducted to examine genetic variation among regions, among populations, and among individuals. Genotypic differentiation was evaluated for each p […]

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Allele frequencies of 15 STR loci in Bosnian and Herzegovinian population

2017
PMCID: 5470122
PMID: 28613042
DOI: 10.3325/cmj.2017.58.250
call_split See protocol

[…] populations, we have implemented Dsw method proposed by Shriver et al (). The neighbor-joining dendrogram was constructed based on genetic distance results (). These calculations were performed using POPTREE software (). […]

library_books

Genetic variation and phylogeographic structure of the cotton aphid, Aphis gossypii, based on mitochondrial DNA and microsatellite markers

2017
Sci Rep
PMCID: 5432507
PMID: 28507345
DOI: 10.1038/s41598-017-02105-4

[…] itochondrial gene, which may reflect more recent events, including population divergence, gene flow and bottleneck. The China cotton aphids separated into two genetic groups as supported by the PCoA, POPTREE, STRUCTURE analysis (Figs , and ) and AMOVA result (Table ). Beside the fact that the ancestor haplotype (H10) of mtDNA from Xinjiang was widely distributed in eastern populations, we also de […]


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POPTREEW institution(s)
Life Science Research Center, Kagawa University, Kagawa, Japan; Department of Biology and the Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, State College, PA, USA; Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
POPTREEW funding source(s)
National Institutes of Health (grant GM020293), JSPS Grants-in-Aids 22570093

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