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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 citations


Genome Sequence of Ralstonia pseudosolanacearum Strains with Compatible and Incompatible Interactions with the Major Tomato Resistance Source Hawaii 7996

Genome Announc
PMCID: 5589544
PMID: 28883150
DOI: 10.1128/genomeA.00982-17
call_split See protocol

[…] s currently classified as a distinct species within the R. solanacearum complex, which comprises strains of phylotypes I and III (). Although they are of putative exotic origin, R. pseudosolanacearum phylotype I isolates are currently disseminated in Brazil (north, northeast, and central regions) and infect mainly Solanaceae crops (tomato, peppers, eggplant, and scarlet eggplant) (, ).In this stud […]


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

PLoS One
PMCID: 5038937
PMID: 27677172
DOI: 10.1371/journal.pone.0163746
call_split See protocol

[…] type 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 of closely rel […]


A novel multilocus variable number tandem repeat analysis typing scheme for African phylotype III strains of the Ralstonia solanacearum species complex

PMCID: 4860299
PMID: 27168969
DOI: 10.7717/peerj.1949
call_split See protocol

[…] 12, RS3L17, RS3L18, RS3L19, RS3L20, RS2BL23, and RS4L26. These markers were designed using publicly available genomes of strains belonging to different RSSC phylotypes.RS2AL03 was identified from the phylotype IIA strain CFBP2957. RS2BL23 was identified from the IIB strain MOLK2. RS1L05, RS1L09, RS1L10, and RS1L12 were identified from the phylotype I strain GMI1000. RS4L26 was identified from the […]


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

Sci Rep
PMCID: 4648088
PMID: 26574165
DOI: 10.1038/srep16897

[…] the old sequences was observed in the tree topologies. We have investigated and described this basal clustering in further detail elsewhere. Detailed analyses of the inferred tree topologies with the PhyloType application confirmed the strong panmixia pattern of subtype C strains from southern African countries. The large ML tree could identify monophyletic clusters containing most of the East-Afr […]


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

PLoS One
PMCID: 4368793
PMID: 25793402
DOI: 10.1371/journal.pone.0120389
call_split See protocol

[…] ration 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 ( […]


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

PLoS One
PMCID: 4214637
PMID: 25357201
DOI: 10.1371/journal.pone.0109296
call_split See protocol

[…] 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 se […]


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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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