POPTREEW protocols

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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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Documentation


Maintainer


  • person_outline Naoko Takezaki <>

Publication for POPTREEW

POPTREEW in pipeline

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

[…] 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 […]


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POPTREEW in publications

 (14)
PMCID: 5607197
PMID: 28931071
DOI: 10.1371/journal.pone.0185161

[…] 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 […]

PMCID: 5519200
PMID: 28692692
DOI: 10.1371/journal.pntd.0005749

[…] was used to identify migrant individuals []., to visualize relationships among populations, a neighbor-joining tree was constructed based on fst genetic distance using 100 bootstrap replications in poptree2 []. the fst is one of the well-known parameters used in measuring genetic differentiation between populations using microsatellite data []. the s. japonicum yamanashi strain was used […]

PMCID: 5384763
PMID: 28388618
DOI: 10.1371/journal.pone.0175085

[…] were illustrated using clumpak []., the evolutionary relationship among atlantic sturgeon collections based on the microsatellite data was visualized through the construction of upgma trees in poptree2 []. to further describe among population differentiation based on the microsatellite data, we used the hierarchical amova approach as described above., as a result of its small number […]

PMCID: 5064932
PMID: 27737705
DOI: 10.1186/s13071-016-1811-z

[…] carried out using a matrix of pair-wise genetic distances between individuals calculated []. a phylogenetic tree based on allele frequency data was constructed using the neighbour-joining method in poptree2 []. bootstrap test was calculated with 1,000 replicates., historical dispersal routes in na and recent invasion routes in eu were explored using a bayes factor approach [] in migrate 3.6.10 […]

PMCID: 5037466
PMID: 27670673
DOI: 10.1038/srep34369

[…] the genescan 500 liz (ab) as an internal size standard and 1 to 2 μl of pcr product (1:20 dilution). genotypes were resolved in genemapper version 5.0 (ab). allele frequencies were estimated in poptreew, and an unrooted neighbor-joining (nj) tree of populations was constructed based on the da distance; this distance has been found to be an appropriate measure for obtaining the correct […]


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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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