PhyloType specifications


Unique identifier OMICS_24690
Name PhyloType
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline François Chevenet <>
  • person_outline Olivier Gascuel <>

Publication for PhyloType

PhyloType in publications

PMCID: 5038937
PMID: 27677172
DOI: 10.1371/journal.pone.0163746

[…] c. the tree was constructed with hky+gamma site rate variation in a mpi version of raxml. reliability of internal nodes was evaluated by 100 bootstrap replicates. phylogenies were analysed using phylotype software application [] in order to detect any clustering of sequences with high bootstrap values (>90%) and low sequence diversity (<3%). this was performed to identify pairs […]

PMCID: 4648088
PMID: 26574165
DOI: 10.1038/srep16897

[…] imported into figtree v 1.3.1 ( and manually investigated. the clustering of southern african isolates with other sequences was assessed with the use of the phylotype software application. clusters of five or more sequences from each country were identified with alrt >0.9 and bootstrap >70%., all of the sequences that were generated from old […]

PMCID: 4368793
PMID: 25793402
DOI: 10.1371/journal.pone.0120389

[…] and shifts in viral populations by analyzing data generated from the two time points sequenced for case1. all analyses as described above was applied to the complete dataset and illustrated in phylotype ([]. sequences and their annotations (compartment and time point) were analyzed with the following criteria; size (5), persistence (1), size/difference in population size […]

PMCID: 4214637
PMID: 25357201
DOI: 10.1371/journal.pone.0109296

[…] figtree v 1.3.1 ( to identify potential clusters of capetonian sequences. phylogenies were analysed visually in figtree v 1.3.1 and with the aid of the phylotype software application interface . clusters were identified based on the geographical annotation of taxa with all sequences annotated according to their country of origin. all south african […]

PMCID: 3970142
PMID: 24618811
DOI: 10.3390/v6031112

[…] the prc method confirmed that the seov-hubei clade and the htnv-guizhou clade have diversified more rapidly than lineages in the rest of the tree. , parsimony reconstructions as implemented in phylotype, yielded nearly identical results for both s and m segments phylogenies independently of the optimization method used (acctran or deltran) (, ). , five phylotypes were identified […]

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PhyloType institution(s)
Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS – Universite Montpellier, Montpellier, France; MIVEGEC, CNRS 5290, IRD 224, Universite Montpellier, Montpellier, France; TransVIHMI, UMI233, IRD – Universite Montpellier, Montpellier, France; Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Durban, South Africa
PhyloType funding source(s)
Supported by the HIVphyML project (NRF South Africa and CNRS France); PhyloSpace project (ANR 6eme Extinction); NUMEV Montpellier Labex; and Wellcome Trust (grant 082384/Z/07/Z).

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