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FastML: a web server for probabilistic reconstruction of ancestral sequences
Haim Ashkenazy1, Osnat Penn, Adi Doron-Faigenboim
1Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel.
Nucleic Acids Research
|June 5, 2012
Summary
FastML is a new web server for reconstructing ancestral sequences. It integrates insertions/deletions (indels) and character data, accounts for uncertainty, and supports diverse evolutionary models for evolutionary studies.
Area of Science:
- Evolutionary biology
- Bioinformatics
- Computational biology
Background:
- Ancestral sequence reconstruction is crucial for understanding evolutionary processes.
- Existing tools often have limitations in handling insertions/deletions (indels) and evolutionary model diversity.
Purpose of the Study:
- To introduce FastML, a user-friendly web server for accurate ancestral sequence reconstruction.
- To provide a tool that integrates indel data, accounts for state uncertainty, and supports multiple evolutionary models.
Main Methods:
- Developed FastML, a web server implementing an indel-coding method with a continuous time Markov process for ancestral indel states.
- Incorporated methods to quantify uncertainty in ancestral states, including posterior probabilities and sequence sampling.
- Integrated a wide range of evolutionary models applicable to nucleotide, protein, and codon sequences.
Main Results:
- FastML successfully reconstructs ancestral sequences by integrating both indel and character data.
- The tool provides posterior probabilities for states and samples from the posterior distribution, addressing uncertainty.
- Demonstrated utility through reconstruction of HIV-1 Env protein ancestral sequences.
Conclusions:
- FastML offers a comprehensive and user-friendly solution for ancestral sequence reconstruction.
- Its novel features, including indel coding and uncertainty handling, advance evolutionary studies.
- The web server is freely available to academic users, promoting broader research accessibility.
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