Phylomatic pipeline

Phylomatic specifications

Information


Unique identifier OMICS_08886
Name Phylomatic
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Campbell O. Webb <>

Information


Unique identifier OMICS_08886
Name Phylomatic
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Campbell O. Webb <>

Publication for Phylomatic

Phylomatic IN pipelines

 (7)
2017
PMCID: 5733559
PMID: 29321791
DOI: 10.3389/fpls.2017.02134

[…] each family, the positions of species were resolved with the barcode sequence data. according to this method, a phylogenetic tree was first generated for the sampled species using the online program phylomatic (webb and donoghue, 2005). this tree specified the taxonomic relationship of the 32 families, but within each family species were arrayed as a polytomy. the topology of this tree […]

2016
PMCID: 5051821
PMID: 27706173
DOI: 10.1371/journal.pone.0162907

[…] muscle v.3.8.31 [38] and refined manually using mega v.6.05 [39]. the four gene alignments were then concatenated using seqstate v.1.4.1 [40]., phylogenetic branch lengths were estimated on the phylomatic cladogram from the molecular matrix by maximum likelihood using raxml v.8.0.0 [29]. the raxml output from the original 425 family maximum likelihood tree showed extreme molecular rate […]

2015
PMCID: 4446313
PMID: 26018568
DOI: 10.1371/journal.pone.0126524

[…] alignment altogether represents 91% of native genera in britain (according to plantatt; [17]). we constructed a family-level constraint tree based on the apg iii classification [18] included with phylomatic [19]. after these analyses were performed, fourteen of the sequences were found to have sequencing errors that caused frame-shifts at the extreme 3′ end of the sequences. the corrected […]

2013
PMCID: 3729948
PMID: 23936268
DOI: 10.1371/journal.pone.0071464

[…] had a bootstrap node support >80. below the family level, most of the genera appeared well resolved although with lower bootstrap support values. we then used the apgiii phylogeny as generated by phylomatic as our family level backbone phylogeny and resolved the within family phylogenetic classification by adding the results obtained from the rbcl phylogeny. branch lengths and dated nodes […]

2009
PMCID: 2740862
PMID: 19763265
DOI: 10.1371/journal.pone.0007071

[…] files., i created a phylogeny for all the herbaceous old field plants i surveyed by combining a backbone tree based on the apg phylogeny (http://www.mobot.org/mobot/research/apweb/) generated by phylomatic (http://www.phylodiversity.net/phylomatic/phylomatic.html) with subtrees created using downloaded sequences. i made three such trees for three families that lacked resolution […]

Phylomatic institution(s)
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA

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