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PhyloType specifications

Information


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

Documentation


Maintainers


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

Publication for PhyloType

PhyloType citations

 (6)
library_books

Genome Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance

2016
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 […]

library_books

History and origin of the HIV 1 subtype C epidemic in South Africa and the greater southern African region

2015
PMCID: 4648088
PMID: 26574165
DOI: 10.1038/srep16897

[…] imported into figtree v 1.3.1 (http://tree.bio.ed.ac.uk/software/figtree) 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 […]

library_books

Evidence of Long Lived Founder Virus in Mother to Child HIV Transmission

2015
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 (www.phylotype.org)[]. sequences and their annotations (compartment and time point) were analyzed with the following criteria; size (5), persistence (1), size/difference in population size […]

library_books

Detection of Transmission Clusters of HIV 1 Subtype C over a 21 Year Period in Cape Town, South Africa

2014
PMCID: 4214637
PMID: 25357201
DOI: 10.1371/journal.pone.0109296

[…] figtree v 1.3.1 (http://www.tree.bio.ed.ac.uk/software/figtree/) 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 […]

library_books

Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae Associated Hantaviruses

2014
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 […]

library_books

Is ecological speciation a major trend in aphids? Insights from a molecular phylogeny of the conifer feeding genus Cinara

2013
PMCID: 3848992
PMID: 24044736
DOI: 10.1186/1742-9994-10-56

[…] geographic isolation in the speciation processes. we first investigated how geographic areas, host ranges and feeding sites were distributed along our phylogeny using the recently developed software phylotype []. given the distributions of characters across a set of taxa and a phylogeny, phylotype determines if taxa sharing the same character states are more clustered than expected by chance […]


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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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