ArticleNucleic acids research2012
FastML: a web server for probabilistic reconstruction of ancestral sequences.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 211 papers.
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211 citing papers in PubMed.
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- Structural and evolutionary determinants of Argonaute function.Nucleic acids research · 2025Article
- Exploring the Stability and Substrate Profile of Transaminase from Silicibacter pomeroyi with Ancestral Sequence Reconstruction.Chembiochem : a European journal of chemical biology · 2025Article
- Algorithms to reconstruct past indels: The deletion-only parsimony problem.PLoS computational biology · 2025Article
- Impact of Phylogenetic Method Choice on Indel Analyses in HIV-1 Subtype B.Genome biology and evolution · 2025Article
- Widespread and Convergent Evolution of Cone Monochromacy in Galeomorph Sharks.Molecular biology and evolution · 2025Article
- Recent advances on protein engineering for improved stability.Biodesign research · 2025Review
- A de novo Gene Promotes Seed Germination Under Drought Stress in Arabidopsis.Molecular biology and evolution · 2025Article
- HIV-1 Vif global diversity and possible APOBEC-mediated response since 1980.Virus evolution · 2025Article
- Ancestral Sequence Reconstruction for Designing Biocatalysts and Investigating their Functional Mechanisms.JACS Au · 2024Review
- Design of ancestral mammalian alkaline phosphatase bearing high stability and productivity.Applied and environmental microbiology · 2024Article
- Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction.BMC bioinformatics · 2024Article
151 more citing papers are in PubMed but not listed here.
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7 authors.
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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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