共 31 条
Searching for virus phylotypes
被引:24
作者:
Chevenet, Francois
[1
,2
,3
]
Jung, Matthieu
[1
,4
]
Peeters, Martine
[4
]
de Oliveira, Tulio
[5
]
Gascuel, Olivier
[1
]
机构:
[1] Univ Montpellier 2, CNRS, UMR 5506, Inst Biol Computat,LIRMM, Montpellier, France
[2] Univ Montpellier I, CNRS 5290, IRD 224, MIVEGEC, Montpellier, France
[3] Univ Montpellier 2, CNRS 5290, IRD 224, MIVEGEC, Montpellier, France
[4] Univ Montpellier I, IRD, UMI233, TransVIHMI, Montpellier, France
[5] Univ KwaZulu Natal, Africa Ctr Hlth & Populat Studies, Durban, South Africa
基金:
英国惠康基金;
关键词:
SUBTYPE C EPIDEMIC;
HIV-1;
PHYLOGENIES;
PHYLOGEOGRAPHY;
IDENTIFICATION;
DISPERSAL;
D O I:
10.1093/bioinformatics/btt010
中图分类号:
Q5 [生物化学];
学科分类号:
071010 ;
081704 ;
摘要:
Motivation: Large phylogenies are being built today to study virus evolution, trace the origin of epidemics, establish the mode of transmission and survey the appearance of drug resistance. However, no tool is available to quickly inspect these phylogenies and combine them with extrinsic traits (e. g. geographic location, risk group, presence of a given resistance mutation), seeking to extract strain groups of specific interest or requiring surveillance. Results: We propose a new method for obtaining such groups, which we call phylotypes, from a phylogeny having taxa (strains) annotated with extrinsic traits. Phylotypes are subsets of taxa with close phylogenetic relationships and common trait values. The method combines ancestral trait reconstruction using parsimony, with combinatorial and numerical criteria measuring tree shape characteristics and the diversity and separation of the potential phylotypes. A shuffling procedure is used to assess the statistical significance of phylotypes. All algorithms have linear time complexity. This results in low computing times, typically a few minutes for the larger data sets with a number of shuffling steps. Two HIV-1 data sets are analyzed, one of which is large, containing > 3000 strains of HIV-1 subtype C collected worldwide, where the method shows its ability to recover known clusters and transmission routes, and to detect new ones.
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页码:561 / 570
页数:10
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