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. 2012 Jul;40(Web Server issue):W580-4.
doi: 10.1093/nar/gks498. Epub 2012 May 31.

FastML: a web server for probabilistic reconstruction of ancestral sequences

Haim Ashkenazy  1 , Osnat Penn, Adi Doron-Faigenboim, Ofir Cohen, Gina Cannarozzi, Oren Zomer, Tal Pupko
Affiliations

FastML: a web server for probabilistic reconstruction of ancestral sequences

Haim Ashkenazy et al. Nucleic Acids Res. 2012 Jul.

Abstract

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/.

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Figures

Figure 1.
Figure 1.
A schematic flow chart of the FastML web server.
Figure 2.
Figure 2.
An example of the FastML output. Graphical representation of the marginal posterior probabilities of the reconstruction of HIV-1 Env ancestral sequences of (A) subtype B ancestor and (B) subtype C ancestor. A red rectangle highlights the different in the reconstruction of position 592 in the MSA, as discussed in the text.
See this image and copyright information in PMC

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