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TREE-PUZZLE specifications


Unique identifier OMICS_18458
Alternative name tree-ppuzzle
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 5.3
Stability Stable
Source code URL
Maintained Yes




No version available



  • person_outline Heiko Schmidt
  • person_outline Arndt von Haeseler

Publication for TREE-PUZZLE

TREE-PUZZLE citations


A phylogenomic framework and timescale for comparative studies of tunicates

BMC Biol
PMCID: 5899321
PMID: 29653534
DOI: 10.1186/s12915-018-0499-2

[…] xenoturbellid as more distant outgroups. When several sequences were available for a given OTU, the slowest evolving one was selected by SCaFoS, according to maximum likelihood distances computed by TREE-PUZZLE [] under a WAG+F model. The percentage of missing data per taxon was reduced by creating some chimerical sequences from closely related species (i.e. Eptatretus burgeri/ Myxine glutinosa, […]


Genome Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.)

PMCID: 5867889
PMID: 29547590
DOI: 10.3390/genes9030168

[…] ( []. A Bayesian Inference tree (BI tree) was generated using the MrBayes program and ModelGenerator software []. Finally, the optimum topology was chosen using Tree-puzzle-5.3 and CONSEL software []. […]


Distribution of endangered Italian gudgeon Romanogobio benacensis (Cypriniformes, Cyprinidae, Gobioninae) with remarks on distinguishing morphological characters

PMCID: 5806454
PMID: 29430207
DOI: 10.3897/zookeys.729.20615
call_split See protocol

[…] se SH tests (, , ); SH – Shimodaira-Hasegawa test (2000); ELW – Expected Likelihood Weight (Strimmer-Rambaut 2002); 2sKH – two sided Kishino-Hasegawa test (1989)]. All topology tests were computed in TREE-PUZZLE v5.3rc16 (). […]


Discovery of Culex pipiens associated tunisia virus: a new ssRNA(+) virus representing a new insect associated virus family

Virus Evol
PMCID: 5763275
PMID: 29340209
DOI: 10.1093/ve/vex040

[…] sing PhyML () and robustness of nodes was assessed with aLRT statistics (SH-like branch supports) (). Shimodaira–Hasegawa (SH) () and a one-sided Kishino-Hasegawa (1sKH) () tests were performed using TREE-PUZZLE (version 5.6.rc16) () to detect possible phylogenetic incongruence between different domains of the same ORF. […]


Biological and phylogenetic characteristics of West African lineages of West Nile virus

PLoS Negl Trop Dis
PMCID: 5695850
PMID: 29117195
DOI: 10.1371/journal.pntd.0006078

[…] luding lineage 6, which there is only a partial sequence available) were included to compare genetic percent identities.Likelihood mapping analyses for estimation of data quality were performed using Tree-Puzzle (Quartets ranged between 10,000 and 40,000) [,]. For each alignment we performed recombination screening (RDP, GeneConv, Chimaera, MaxChi, BootScan and SiScan) in RDP4.61 [].The Bayesian p […]


Archigregarines of the English Channel revisited: New molecular data on Selenidium species including early described and new species and the uncertainties of phylogenetic relationships

PLoS One
PMCID: 5669490
PMID: 29099876
DOI: 10.1371/journal.pone.0187430
call_split See protocol

[…] haustive sampling of Selenidiidae s.s. (as defined by []), as well as other archigregarine taxa (81 taxa, 1601 sites) rooted with marine eugregarines. Homogeneity of base-composition was tested using Tree-Puzzle 5.3 []. Root-to-tip distances for main clades of the dataset were measured using the TreeStat 1.2 ( the 18S rDNA of several gregarine ta […]


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TREE-PUZZLE institution(s)
Max-Planck-Institut fur Molekulare Genetik, Berlin, Germany; University of Oxford, Department of Zoology, Oxford, UK; Max-Planck-Institut fur Evolutionare Anthropologie, Leipzig, Germany
TREE-PUZZLE funding source(s)
Supported by Deutsche Forschungs– gemeinschaft and the Max Planck Society.


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