PhyloWS statistics

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Citations per year

Citations chart

Popular tool citations

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Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases


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PhyloWS specifications


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



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

Additional information

PhyloWS in pipelines

PMCID: 4815069
PMID: 27036298
DOI: 10.1186/s12864-016-2599-0

[…] the consensus tree was drawn using figtree v1.4.2 ( the phylogenetic analysis results are deposited in treebase ( and dryad digital repository (doi:10.5061/dryad.674p4)., the fungal pathogenicity genes were retrieved from the pathogen-host interaction (phi) database [] […]

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:, we used blastp to generate percent identities and similarities for predicted amino acid sequences of orthologs between species. we used only sequences […]

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; 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 […]

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 (, 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 […]

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 (, 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

PMCID: 5895190
PMID: 29732262
DOI: 10.1002/aps3.1032

[…] locus sets. concatenated alignments for each locus set are available in the dryad digital repository (; chau et al., ) and treebase (, 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 (, 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:, 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,, 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 (, 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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PhyloWS reviews

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