tree-puzzle specifications

Information


Unique identifier OMICS_18458
Name tree-puzzle
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 http://www.tree-puzzle.de/tree-puzzle-5.3.rc16.tar.gz
Maintained Yes

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Documentation


Maintainers


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

tree-puzzle article

tree-puzzle citations

 (5)
2016
PMCID: 5073338

[…] 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. […]

2016
PMCID: 4997794

[…] sequence data., to obtain an overall impression of the phylogenetic signals in the hiv-2 pol gene group b dataset, a likelihood-mapping analysis, undertaken of 10,000 random quartets generated using tree puzzle was carried out as already described.[20] a likelihood map consists of an equilateral triangle containing dots representing the likelihoods of the three possible un-rooted trees for a set […]

2013
PMCID: 3913041

[…] 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 […]

2013
PMCID: 3913041

[…] 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 […]

2007
PMCID: 2241609

[…] on kimura's two parameter model distances using the treecon program [65]. maximum-likelihood and mp trees were computed using the wag+f model plus a gamma distribution with four categories using the tree-puzzle [66] and mega 3.1 program [67], respectively. all trees were bootstrapped 100 times [68], unless otherwise indicated., the character compatibility analysis was performed on a concatenated […]

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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