FastML: a web server for probabilistic reconstruction of ancestral sequences

被引:242
作者
Ashkenazy, Haim [1 ]
Penn, Osnat [1 ]
Doron-Faigenboim, Adi [3 ]
Cohen, Ofir [1 ]
Cannarozzi, Gina [2 ]
Zomer, Oren [1 ]
Pupko, Tal [1 ]
机构
[1] Tel Aviv Univ, George S Wise Fac Life Sci, Dept Cell Res & Immunol, IL-69978 Tel Aviv, Israel
[2] Univ Bern, Inst Plant Sci, CH-3013 Bern, Switzerland
[3] ARO, Volcani Ctr, Inst Plant Sci, IL-50250 Bet Dagan, Israel
基金
以色列科学基金会;
关键词
AMINO-ACID-SEQUENCES; MITOCHONDRIAL-DNA; PHYLETIC PATTERNS; PROTEIN SEQUENCES; INFERENCE; MODEL; SUBSTITUTION; SITES; DIVERSITY; ALGORITHM;
D O I
10.1093/nar/gks498
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Ancestral sequence reconstruction is essential to a variety of evolutionary studies. Here, we present the FastML web server, a user-friendly tool for the reconstruction of ancestral sequences. FastML implements various novel features that differentiate it from existing tools: (i) FastML uses an indel-coding method, in which each gap, possibly spanning multiples sites, is coded as binary data. FastML then reconstructs ancestral indel states assuming a continuous time Markov process. FastML provides the most likely ancestral sequences, integrating both indels and characters; (ii) FastML accounts for uncertainty in ancestral states: it provides not only the posterior probabilities for each character and indel at each sequence position, but also a sample of ancestral sequences from this posterior distribution, and a list of the k-most likely ancestral sequences; (iii) FastML implements a large array of evolutionary models, which makes it generic and applicable for nucleotide, protein and codon sequences; and (iv) a graphical representation of the results is provided, including, for example, a graphical logo of the inferred ancestral sequences. The utility of FastML is demonstrated by reconstructing ancestral sequences of the Env protein from various HIV-1 subtypes. FastML is freely available for all academic users and is available online at http://fastml.tau.ac.il/.
引用
收藏
页码:W580 / W584
页数:5
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