PhyloTreePruner statistics

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PhyloTreePruner specifications

Information


Unique identifier OMICS_04250
Name PhyloTreePruner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PhyloTreePruner

PhyloTreePruner in pipeline

2018
PMCID: 5932825
DOI: 10.1186/s12862-018-1142-0

[…] v0.5-devel with nucleotide sequences as input (https://bitbucket.org/caseywdunn/agalma) as in zapata et al. [] and, 2) a custom phylogenomics pipeline consisting of orthofinder v0.4.0 [] followed by phylotreepruner [] and our associated wrapper scripts that we refer to as of-ptp. of-ptp takes the transdecoder-translated peptide sequences from each transcriptome as input. the final supermatrices […]


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PhyloTreePruner in publications

 (7)
PMCID: 5932825
DOI: 10.1186/s12862-018-1142-0

[…] cnidarian clades to the construction and analyses of independent phylogenomic datasets for cnidaria using two popular approaches: 1) agalma [] and 2) a custom pipeline based on orthofinder [] and phylotreepruner []. we show that both procedures produce datasets with surprisingly little overlap in terms of data composition, but resolve the same topology under robust phylogenetic methods. […]

PMCID: 5906903
PMID: 29617768
DOI: 10.1093/gigascience/giy034

[…] model []. rapid bootstrap analysis and search for the best­scoring maximum-likelihood (ml) tree within one program run with 100 rapid bootstrap replicates was used. the trees were pruned using phylotreepruner v1.0 [] to remove paralogues, with 0.5 as the bootstrap cutoff and a minimum of 20 species in the orthogroup after pruning for inclusion in the supermatrix. where species […]

PMCID: 5700196
PMID: 29167427
DOI: 10.1038/s41467-017-01927-0

[…] using the circos software. the orthomcl pipeline was used to define gene families for the selected species. for phylogenetic analysis, we selected orthologous genes using a tree-based approach phylotreepruner, and the phylogenetic tree was constructed using raxml. to estimate the divergence time for c. farreri and other metazoans, the first and second codon positions of the orthologs […]

PMCID: 5664179
PMID: 28993654
DOI: 10.1038/s41559-017-0331-3

[…] of 1,000. after alignment, an approximately maximum likelihood tree was generated for each og with fasttree 2 using “slow” and “gamma” options. each tree and corresponding og was processed with phylotreepruner to screen for paralogs; a bootstrap value of 90 was used for collapsing nodes. if more than one sequence for any of the six respective species was present after the paralog pruning […]

PMCID: 5450073
PMID: 28558722
DOI: 10.1186/s12862-017-0973-4

[…] approach to remove likely paralogs from our alignments. we inferred a maximum-likelihood (ml) tree for each aligned orthogroup with fasttreemp [] (under the –slow and –gamma settings), and used phylotreepruner [] to screen each of the resulting trees. in phylotreepruner, nodes on each ml tree with sh-like local support values <0.7 were collapsed into polytomies, and the largest subtree […]


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PhyloTreePruner institution(s)
Department of Biological Sciences, Auburn University, Auburn, USA

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