Literature DB >> 1556741

Inching toward reality: an improved likelihood model of sequence evolution.

J L Thorne1, H Kishino, J Felsenstein.   

Abstract

Our previous evolutionary model is generalized to permit approximate treatment of multiple-base insertions and deletions as well as regional heterogeneity of substitution rates. Parameter estimation and alignment procedures that incorporate these generalizations are developed. Simulations are used to assess the accuracy of the parameter estimation procedure and an example of an inferred alignment is included.

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Year:  1992        PMID： 1556741     DOI： 10.1007/bf00163848

Source DB:  PubMed          Journal:  J Mol Evol        ISSN： 0022-2844            Impact factor:   2.395


  12 in total

1.  Optimal sequence alignments.

Authors:  W M Fitch; T F Smith
Journal:  Proc Natl Acad Sci U S A       Date:  1983-03       Impact factor: 11.205

2.  An evolutionary model for maximum likelihood alignment of DNA sequences.

Authors:  J L Thorne; H Kishino; J Felsenstein
Journal:  J Mol Evol       Date:  1991-08       Impact factor: 2.395

3.  16S rRNA sequence indicates that plant-pathogenic mycoplasmalike organisms are evolutionarily distinct from animal mycoplasmas.

Authors:  P O Lim; B B Sears
Journal:  J Bacteriol       Date:  1989-11       Impact factor: 3.490

4.  Unified approach to alignment and phylogenies.

Authors:  J Hein
Journal:  Methods Enzymol       Date:  1990       Impact factor: 1.600

5.  Maximum likelihood alignment of DNA sequences.

Authors:  M J Bishop; E A Thompson
Journal:  J Mol Biol       Date:  1986-07-20       Impact factor: 5.469

6.  Eubacterial origin of chlamydiae.

Authors:  W G Weisburg; T P Hatch; C R Woese
Journal:  J Bacteriol       Date:  1986-08       Impact factor: 3.490

7.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

Authors:  M Kimura
Journal:  J Mol Evol       Date:  1980-12       Impact factor: 2.395

8.  Comparative biosequence metrics.

Authors:  T F Smith; M S Waterman; W M Fitch
Journal:  J Mol Evol       Date:  1981       Impact factor: 2.395

9.  An improved algorithm for matching biological sequences.

Authors:  O Gotoh
Journal:  J Mol Biol       Date:  1982-12-15       Impact factor: 5.469

10.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.

Authors:  M Hasegawa; H Kishino; T Yano
Journal:  J Mol Evol       Date:  1985       Impact factor: 2.395
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  70 in total

Review 1.  Evolution of genes and taxa: a primer.

Authors:  J J Doyle; B S Gaut
Journal:  Plant Mol Biol       Date:  2000-01       Impact factor: 4.076

2.  The effects of rate variation on ancestral inference in the coalescent.

Authors:  L Markovtsova; P Marjoram; S Tavaré
Journal:  Genetics       Date:  2000-11       Impact factor: 4.562

3.  The age of a unique event polymorphism.

Authors:  L Markovtsova; P Marjoram; S Tavaré
Journal:  Genetics       Date:  2000-09       Impact factor: 4.562

4.  Markov chain Monte Carlo without likelihoods.

Authors:  Paul Marjoram; John Molitor; Vincent Plagnol; Simon Tavare
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-08       Impact factor: 11.205

5.  MAVID: constrained ancestral alignment of multiple sequences.

Authors:  Nicolas Bray; Lior Pachter
Journal:  Genome Res       Date:  2004-04       Impact factor: 9.043

6.  MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution.

Authors:  Peter D Keightley; Toby Johnson
Journal:  Genome Res       Date:  2004-03       Impact factor: 9.043

7.  A stochastic evolutionary model for protein structure alignment and phylogeny.

Authors:  Christopher J Challis; Scott C Schmidler
Journal:  Mol Biol Evol       Date:  2012-06-21       Impact factor: 16.240

8.  Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences.

Authors:  Sang Chul Choi; Benjamin D Redelings; Jeffrey L Thorne
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2008-12-27       Impact factor: 6.237

9.  Genome-wide nucleotide-level mammalian ancestor reconstruction.

Authors:  Benedict Paten; Javier Herrero; Stephen Fitzgerald; Kathryn Beal; Paul Flicek; Ian Holmes; Ewan Birney
Journal:  Genome Res       Date:  2008-10-10       Impact factor: 9.043

10.  Neisseria weaveri sp. nov., formerly CDC group M-5, a gram-negative bacterium associated with dog bite wounds.

Authors:  B M Andersen; A G Steigerwalt; S P O'Connor; D G Hollis; R S Weyant; R E Weaver; D J Brenner
Journal:  J Clin Microbiol       Date:  1993-09       Impact factor: 5.948
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