ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2008
A model of evolution and structure for multiple sequence alignment.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
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- Epistasis among clustered lineage-specific adaptive amino acid substitutions in the Drosophila Trio protein.bioRxiv : the preprint server for biology · 2025Article
- Putting hornets on the genomic map.Scientific reports · 2023Article
- Pangenome and genomic taxonomy analyses of Leuconostoc gelidum and Leuconostoc gasicomitatum.BMC genomics · 2022Article
- The Impact of Fast Radiation on the Phylogeny ofInsects · 2022Article
- New data on Henneguya postexilis Minchew, 1977, a parasite of channel catfish Ictalurus punctatus, with notes on resolution of molecular markers for myxozoan phylogeny.Systematic parasitology · 2022Article
- Viviparity and habitat restrictions may influence the evolution of male reproductive genes in tsetse fly (Glossina) species.BMC biology · 2021Article
- A NEW SPECIES OF MYXOBOLUS (CNIDARIA: MYXOSPOREA: MYXOBOLIDAE) FROM THE BLUE SUCKER, CYCLEPTUS ELONGATUS (LESUEUR) (CYPRINIFORMES: CATOSTOMIDAE: CYCLEPTINAE), FROM ARKANSAS.The Journal of parasitology · 2021Article
- The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment.Systematic biology · 2021Article
- Host-Virus Arms Races Drive Elevated Adaptive Evolution in Viral Receptors.Journal of virology · 2020Article
- Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency.Genome biology · 2019Article
- Evolution ofCommunications biology · 2019Article
- Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions.Genome biology · 2018Article
- High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites.PLoS genetics · 2017Article
- Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum.BMC genomics · 2016Article
- Article
- Insights into the evolution of longevity from the bowhead whale genome.Cell reports · 2015Article
- Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system.BMC bioinformatics · 2014Article
- Linking genomics and ecology to investigate the complex evolution of an invasive Drosophila pest.Genome biology and evolution · 2013Article
- Nucleotide diversity of a genomic sequence similar to SHATTERPROOF (PvSHP1) in domesticated and wild common bean (Phaseolus vulgaris L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed a phylogeny-aware progressive alignment method that recognizes insertions and deletions as distinct evolutionary events and thus avoids systematic errors created by traditional alignment methods. We now extend this method to simultaneously model regional heterogeneity and evolution. This novel method can be flexibly adapted to alignment of nucleotide or amino acid sequences evolving under processes that vary over genomic regions and, being fully probabilistic, provides an estimate of regional heterogeneity of the evolutionary process along the alignment and a measure of local reliability of the solution. Furthermore, the evolutionary modelling of substitution process permits adjusting the sensitivity and specificity of the alignment and, if high specificity is aimed at, leaving sequences unaligned when their divergence is beyond a meaningful detection of homology.
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