ArticlePLoS computational biology2009
Fast statistical alignment.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 papers.
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180 citing papers in PubMed.
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- HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes.Genome biology · 2025Article
- Evolution of developmental bias explains divergent patterns of phenotypic evolution in two nematode clades.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents.Genome biology and evolution · 2025Article
- Phylogenomics supports a single origin of terrestriality in isopods.Proceedings. Biological sciences · 2024Article
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- Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts.PLoS genetics · 2024Article
- The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes.PLoS genetics · 2024Article
- Total substitution and partial modification of the set of non-ribosomal peptide synthetases clusters lead to pyoverdine diversity in theFrontiers in microbiology · 2024Article
- Ancient diversity in host-parasite interaction genes in a model parasitic nematode.Nature communications · 2023Article
- Biochemical, functional and genomic characterization of a new probiotic Ligilactobacillus salivarius F14 from the gut of tribes of Odisha.World journal of microbiology & biotechnology · 2023Article
- Convergent and complementary selection shaped gains and losses of eusociality in sweat bees.Nature ecology & evolution · 2023Article
- Evolution is not Uniform Along Coding Sequences.Molecular biology and evolution · 2023Article
- A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data.Molecular biology and evolution · 2023Article
- Adaptive duplication and genetic diversification of protein kinase R contribute to the specificity of bat-virus interactions.Science advances · 2022Article
- A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus).American journal of botany · 2022Article
- Article
- Toward the robust resolution of taxonomic ambiguity within Lepocinclis (Euglenida) based on DNA sequencing and morphology.Journal of phycology · 2022Article
120 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches--yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/.
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