TREE-PUZZLE protocols

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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



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  • person_outline Heiko Schmidt <>
  • person_outline Arndt von Haeseler <>

Publication for TREE-PUZZLE

TREE-PUZZLE in pipelines

PMCID: 5577849
PMID: 28854898
DOI: 10.1186/s12864-017-4060-4

[…] species. the orthologous proteins were aligned with the program muscle (ver. 3.8.31) [], and the concatenated amino acid sequences were used to generate a maximum likelihood tree using the program tree-puzzle []. for pairwise syntenic analysis of genome structures, the scaffolds of the paired genomes of c. cicadae, c. militaris and i. fumosorosea were oriented by megablast and argo genome […]

PMCID: 4986183
PMID: 27527502
DOI: 10.1186/s12864-016-2974-x

[…] of orthologous sequences were concatenated using a perl script fasconcat (v1.02, with default parameters) [], and a maximum likelihood phylogenetic tree was created using the dayhoff model in tree-puzzle v5.3.rc16 [] with 1000 bootstrap replicates. the tree was visualized using figtree v1.42 (, antismash, antibiotics & secondary metabolite […]

PMCID: 5073338
PMID: 27767073
DOI: 10.1038/srep35822

[…] information contained in the dataset, likelihood-mapping analysis, based on the maximum-likelihood values for the three possible unrooted trees of four randomly chosen sequences, was performed using tree-puzzle v5.3, in which all possible quartets for each of the six lineages representing specific epidemics were analyzed. the analysis was then repeated for the entire genealogy. for each quartet, […]

PMCID: 4610023
PMID: 26451642
DOI: 10.1186/1471-2105-16-S14-S8

[…] treepuzzling: support for the l27 and pdz domains was further evaluated by generating a 95% confidence set of trees based on the expected likelihood weight method as implemented in consel []. tree-puzzle [] was used to sample 50,000 trees, whose likelihoods were assessed using the jtt model with 4 gamma rate categories. a consensus network was constructed from the l27 confidence set using […]

PMCID: 5635587
PMID: 26454011
DOI: 10.1093/gbe/evv190

[…] tree images., to determine whether trees were significantly different from each other, au () and sh tests () were performed with consel v0.20 (). site likelihoods for each tree were calculated with tree-puzzle version 5.2 () with the options to estimate amino acid frequencies from the data and using gamma distributed rates with four categories and alpha parameter estimated from the data set (, […]

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TREE-PUZZLE in publications

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, […]

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 []. , chromosomal position information for the bnckxs was obtained from the b. napus genome browser, and the genes were mapped onto chromosomal linkage groups […]

PMCID: 5806454
PMID: 29430207
DOI: 10.3897/zookeys.729.20615

[…] 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 ()., comparative morphological analysis of r. benacensis (n = 23), g. gobio (n = 2) and g. obtusirostris (n = 24) was performed based on number of available specimens. see fig. […]

PMCID: 5758900
PMID: 29272370
DOI: 10.1093/gbe/evx268

[…] alignment information and manually edited in mega 7.0 (; ). pairwise evolutionary distances (ped) were calculated using a wag amino acid substitution model and maximum likelihood approach in tree-puzzle (). hierarchical classification was achieved by employing the demarc framework in r (; )., multiple sequence alignments for nucleocapsid, glycoprotein precursor, and polymerase […]

PMCID: 5814470
PMID: 29147783
DOI: 10.1007/s00705-017-3643-3

[…] regions were removed using gblock []. this resulted in a sequence alignment of 751 amino acids (aa). phylogenetic relationships were determined using the maximum-likelihood (ml) method available in tree_puzzle 5.2 (, employing the vt [] model of amino acid substitution. the tree was constructed based on approximate maximum-likelihood values using the selected model […]

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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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