FastML: A web server for probabilistic reconstruction of ancestral sequences

Haim Ashkenazy, Osnat Penn, Adi Doron-Faigenboim, Ofir Cohen, Gina Cannarozzi, Oren Zomer, Tal Pupko

Research output: Contribution to journalArticlepeer-review

237 Scopus citations


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

Original languageEnglish
Pages (from-to)W580-W584
JournalNucleic Acids Research
Issue numberW1
StatePublished - 1 Jul 2012
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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