FastML: a web server for probabilistic reconstruction of ancestral sequences.
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/.
Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel.
Haim
H
Ashkenazy
Osnat
O
Penn
Adi
A
Doron-Faigenboim
Ofir
O
Cohen
Gina
G
Cannarozzi
Oren
O
Zomer
Tal
T
Pupko
D003196:Computer Graphics; D054643:INDEL Mutation; D020407:Internet; D010802:Phylogeny; D011336:Probability; D016415:Sequence Alignment; D012984:Software; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics
D054299:env Gene Products, Human Immunodeficiency Virus