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POPTREE2 specifications


Unique identifier OMICS_32218
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Stability Stable
Maintained Yes




No version available



  • person_outline Naoko Takezaki

Publication for POPTREE2

POPTREE2 citations


Strong genetic differentiation in tropical seagrass Enhalus acoroides (Hydrocharitaceae) at the Indo Malay Archipelago revealed by microsatellite DNA

PMCID: 5855881
PMID: 29576933
DOI: 10.7717/peerj.4315

[…] differentiation was estimated between pairs of populations with the estimator θ () as implemented in Arlequin ver. 3.5.1 (). Second, we inferred the phylogenetic relationship among populations using Poptree2 () with the Neighbor Joining method () using Nei’s DA distance () and 1,000 bootstrapping replicates. Tree topology was rooted using Mega 5 ().Third, we used Structure 2.3.4 () to infer popul […]


Phylogeography of the termite Macrotermes gilvus and insight into ancient dispersal corridors in Pleistocene Southeast Asia

PLoS One
PMCID: 5706666
PMID: 29186140
DOI: 10.1371/journal.pone.0186690
call_split See protocol

[…] neighbor in the phylip 3.69 package []. Additionally, another NJ tree was reconstructed to view relationships between pre-defined populations groups as inferred from microsat [] using DA distance in poptree2 [] at10,000 bootstrap iterations.The probability of individual assignments to population clusters (K) without prior information about the origin of individuals was calculated using structure […]


A glimpse at the intricate mosaic of ethnicities from Mesopotamia: Paternal lineages of the Northern Iraqi Arabs, Kurds, Syriacs, Turkmens and Yazidis

PLoS One
PMCID: 5669434
PMID: 29099847
DOI: 10.1371/journal.pone.0187408

[…] i Y-STR datasets).A neighbor-joining (N-J) phylogenetic tree based on the Nei’s discriminant analysis (DA) genetic distance metric and the allele frequencies of each dataset was constructed using the POPTREE2 software []. Bootstrap values were calculated based on 10,000 replications. Along with the five novel Y-STR datasets from the current study, the following population datasets with equivalent […]


Geographic strain differentiation of Schistosoma japonicum in the Philippines using microsatellite markers

PLoS Negl Trop Dis
PMCID: 5519200
PMID: 28692692
DOI: 10.1371/journal.pntd.0005749
call_split See protocol

[…] 2.0 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 as an ou […]


The colonization and divergence patterns of Brandt’s vole (Lasiopodomys brandtii) populations reveal evidence of genetic surfing

BMC Evol Biol
PMCID: 5480173
PMID: 28637425
DOI: 10.1186/s12862-017-0995-y

[…] use of Wright’s F ST values. The allelic richness (A r) was calculated for each site population based on a minimum sample size of 14 using the rarefaction procedure implemented in HP-Rare [].We used Poptree2 [] to construct a neighbor-joining (NJ) tree for all Brandt’s vole populations based on the pairwise genetic distances (Da) generated from microsatellite genotypes, and we used a Bayesian MCM […]


Evidence of natural reproduction of Atlantic sturgeon in the Connecticut River from unlikely sources

PLoS One
PMCID: 5384763
PMID: 28388618
DOI: 10.1371/journal.pone.0175085
call_split See protocol

[…] TRUCTURE 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 of famili […]


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POPTREE2 institution(s)
Life Science Research Center, Kagawa University, Ikenobe 1750-1, Kitagun, 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
POPTREE2 funding source(s)
Supported by National Institutes of Health (grant GM020293).

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