tree-puzzle pipeline

tree-puzzle specifications


Unique identifier OMICS_18458
Name tree-puzzle
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: 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) [90], and a maximum likelihood phylogenetic tree was created using the dayhoff model in tree-puzzle v5.3.rc16 [91] with 1000 bootstrap replicates. the tree was visualized using figtree v1.42 (, antismash, antibiotics & secondary metabolite […]

PMCID: 5073338
PMID: 27767073
DOI: 10.1038/srep35822

[…] contained in the dataset, likelihood-mapping analysis16, based on the maximum-likelihood values for the three possible unrooted trees of four randomly chosen sequences, was performed using tree-puzzle v5.317, 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. […]

PMCID: 3913041
PMID: 24075994
DOI: 10.1016/j.celrep.2013.08.031

[…] were generated using clustalx software (larkin et al., 2007), correcting for multiple substitutions and bootstrapped by 1000 repetitions. for ml analysis, consensus trees were calculated, using tree-puzzle (schmidt et al., 2002) (v5.3), from 100 trees generated with iqpnni (vinh and von haeseler, 2004) (v3.3.2) using the blosum62 substitution matrix and 4 categories of gamma-distributed […]

PMCID: 3595036
PMID: 23246794
DOI: 10.1093/gbe/evs122

[…] 2004) and then back-translated to dna. the multiple alignments were concatenated, and phylogenetic reconstruction was performed on this alignment. a maximum likelihood distance matrix was built by tree-puzzle 5.2 (schmidt et al. 2002) under the hasegawa–kishino–yano + γ model. the tree was inferred from the distance matrix using bionj (gascuel 1997). support of the topology was estimated […]

PMCID: 3029252
PMID: 21298028
DOI: 10.1371/journal.pgen.1001284

[…] tree of each clade was reconstructed from the concatenated alignments of genes comprising their core genome. protein alignments were generated using muscle [73] and then back-translated to dna. tree-puzzle [74] was used to generate the matrix of distances by maximum likelihood with the hky+γ model and exact parameter estimates. the trees were then computed from these distance matrices using […]

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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