Literature DB >> 10833195

A fast algorithm for joint reconstruction of ancestral amino acid sequences.

T Pupko1, I Pe'er, R Shamir, D Graur.   

Abstract

A dynamic programming algorithm is developed for maximum-likelihood reconstruction of the set of all ancestral amino acid sequences in a phylogenetic tree. To date, exhaustive algorithms that find the most likely set of ancestral states (joint reconstruction) have running times that scale exponentially with the number of sequences and are thus limited to very few taxa. The time requirement of our new algorithm scales linearly with the number of sequences and is therefore applicable to practically any number of taxa. A detailed description of the new algorithm and an example of its application to cytochrome b sequences are provided.

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Year:  2000        PMID： 10833195     DOI： 10.1093/oxfordjournals.molbev.a026369

Source DB:  PubMed          Journal:  Mol Biol Evol        ISSN： 0737-4038            Impact factor:   16.240


  112 in total

1.  Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates.

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Journal:  Proc Natl Acad Sci U S A       Date:  2002-03-26       Impact factor: 11.205

2.  FastML: a web server for probabilistic reconstruction of ancestral sequences.

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3.  Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons.

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Journal:  Genome Res       Date:  2011-10-05       Impact factor: 9.043

4.  Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.

Authors:  Wayne Delport; Art F Y Poon; Simon D W Frost; Sergei L Kosakovsky Pond
Journal:  Bioinformatics       Date:  2010-07-29       Impact factor: 6.937

5.  Functional evolution of the OAS1 viral sensor: Insights from old world primates.

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Journal:  Infect Genet Evol       Date:  2016-07-05       Impact factor: 3.342

6.  Tropical geometry of statistical models.

Authors:  Lior Pachter; Bernd Sturmfels
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-08       Impact factor: 11.205

7.  Antagonism of SAMHD1 is actively maintained in natural infections of simian immunodeficiency virus.

Authors:  Chelsea J Spragg; Michael Emerman
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-09       Impact factor: 11.205

8.  Reconstructing large regions of an ancestral mammalian genome in silico.

Authors:  Mathieu Blanchette; Eric D Green; Webb Miller; David Haussler
Journal:  Genome Res       Date:  2004-12       Impact factor: 9.043

9.  Evolutionary rate and gene expression across different brain regions.

Authors:  Tamir Tuller; Martin Kupiec; Eytan Ruppin
Journal:  Genome Biol       Date:  2008       Impact factor: 13.583

10.  Evolutionary genetics of human enterovirus 71: origin, population dynamics, natural selection, and seasonal periodicity of the VP1 gene.

Authors:  Kok Keng Tee; Tommy Tsan-Yuk Lam; Yoke Fun Chan; Jon M Bible; Adeeba Kamarulzaman; C Y William Tong; Yutaka Takebe; Oliver G Pybus
Journal:  J Virol       Date:  2010-01-20       Impact factor: 5.103
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