PhyloWS protocols

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Associated diseases

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PhyloWS specifications

Information


Unique identifier OMICS_23512
Name PhyloWS
Alternative name Phyloinformatics Web Services
Software type Application/Script
Interface Application programming interface
Restrictions to use None
Computer skills Advanced
Stability Alpha
Maintained Yes

Documentation


Maintainers


  • person_outline Hilmar Lapp <>
  • person_outline Hilmar Lapp <>

Additional information


http://evoinfo.nescent.org/PhyloWS_FAQ

PhyloWS in pipelines

 (5)
2016
PMCID: 4815069
PMID: 27036298
DOI: 10.1186/s12864-016-2599-0

[…] the consensus tree was drawn using figtree v1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). the phylogenetic analysis results are deposited in treebase (http://purl.org/phylo/treebase/phylows/study/tb2:s19046) and dryad digital repository (doi:10.5061/dryad.674p4)., the fungal pathogenicity genes were retrieved from the pathogen-host interaction (phi) database [] […]

2016
PMCID: 5096308
PMID: 27809760
DOI: 10.1186/s12864-016-3215-z

[…] trees were constructed from the output of the msa from clustalw. the data matrix for all phylogenetic trees was deposited into treebase (study accession url: http://purl.org/phylo/treebase/phylows/study/tb2:s19948)., we used blastp to generate percent identities and similarities for predicted amino acid sequences of orthologs between species. we used only sequences […]

2013
PMCID: 3706601
PMID: 23874503
DOI: 10.1371/journal.pone.0068082

[…] generated sequences have been deposited in genbank, and all accession numbers are listed in ; data matrices and trees have further been deposited in treebase (id13837; http://purl.org/phylo/treebase/phylows/study/tb2:s13837). sequence data were assembled and edited in the program sequencher 5.0 (gene codes corporation, 2006, ann arbor, mi) and aligned with muscle , accessed through the cipres […]

2012
PMCID: 3406010
PMID: 22844246
DOI: 10.1371/journal.pgen.1002820

[…] for all 16 analyzed loci on the mat chromosomes (), data from heterothallic strains were generated specifically for this study, alignments are available from treebase (http://purl.org/phylo/treebase/phylows/study/tb2:s12093), while for the autosomal loci we used available data (). description of the loci, specific primers for their amplification, pcr conditions and procedures for dna sequencing […]

2012
PMCID: 3528665
PMID: 22978470
DOI: 10.1186/1471-2164-13-478

[…] we used phyml v3.0 with an lg substitution model and 100 nonparametric bootstrap replicates []. the data used to build the trees were deposited in treebase ( http://purl.org/phylo/treebase/phylows/study/tb2:s12601)., whole genome alignments were performed using mummer and mummerplot algorithms in mummer [] with default parameters. the gc plot was drawn using dnaplotter (window size: […]


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PhyloWS in publications

 (398)
PMCID: 5895190
PMID: 29732262
DOI: 10.1002/aps3.1032

[…] locus sets. concatenated alignments for each locus set are available in the dryad digital repository (https://doi.org/10.5061/dryad.v6q0p; chau et al., ) and treebase (http://purl.org/phylo/treebase/phylows/study/tb2:s21931)., ml analyses with different locus sets produced trees with different levels of node support (appendix ). the tree from the taxon‐specific data set was substantially […]

PMCID: 5856374
PMID: 29544443
DOI: 10.1186/s12862-018-1145-x

[…] available at ncbi genbank accession numbers mf564057- mf564071. phylogenetic trees, sequence data and alignments used to produce the results are available at treebase (http://purl.org/phylo/treebase/phylows/study/tb2:s21963)., sm, performed most of the experiments and data analysis, da, lb, th, kyl, jh1, mm, performed experiments, contributed to data analysis, jh2, provided critical reagents, […]

PMCID: 5853078
PMID: 29540194
DOI: 10.1186/s12870-018-1259-8

[…] this manuscript as additional files , , and . we have uploaded the sequence data and phylogeny data to the treebase repository with the following study accession url: http://purl.org/phylo/treebase/phylows/study/tb2:s22364., gl, xl and lc conceived and designed the experiments. jj performed most of the experiments. jj, xl and pz made substantial contributions to the data analysis […]

PMCID: 5845233
PMID: 29523201
DOI: 10.1186/s12917-018-1402-7

[…] in the public, commercial, or not-for-profit sectors., the datasets generated and/or analysed during the current study are available in the treebase repository, http://purl.org/phylo/treebase/phylows/study/tb2:s22326., the datasets generated and/or analysed during the current study are not publicly available due to the full clinical files from the animals whose samples were included […]

PMCID: 5840783
PMID: 29510674
DOI: 10.1186/s12864-018-4569-1

[…] kj885621, kj830752, kj749841, kj630904, kf572032, km093858–59, kc119493, kc578685, kp126516, listed in additional file . phylogenetic data were submitted to treebase (http://purl.org/phylo/treebase/phylows/study/tb2:s22322)., ytj, ybw, hjt, ss, lxz contributed sampling and/or lab work, ytj, hjt, rpb contributed to statistical analyses and production of the paper. all authors read and approved […]


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