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PAML: a program for package for phylogenetic analysis by maximum likelihood
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The article was published on 1997-01-01 and is currently open access. It has received 4896 citations till now.read more
Citations
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Dating the early evolution of plants: detection and molecular clock analyses of orthologs
TL;DR: The described cross-species expansion of the reciprocal best BLAST hit method is a time-effective method for ortholog detection, which results in 68% truly orthologous clusters and the procedure specifically enriches single-copy orthologs.
Duplication and diversifying selection among termite antifungal peptides Research Article
Mark S. Bulmer,Ross H. Crozier +1 more
TL;DR: The results suggest that after termicin duplication, certain critical sites have maintained a positive charge in one duplicate and evolved towards neutrality in the other and that positive selection has directed these changes repeatedly and independently.
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Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison with North American and European populations.
TL;DR: The results suggest that PVY PTNRD was recently introduced into Japan more than once, and has expanded throughout Japan from founder populations.
Journal ArticleDOI
Evolution of Bitter Taste Receptors in Humans and Apes
TL;DR: The analysis of the almost complete repertoires of bitter taste receptor genes in human, great apes, and two Old World monkeys shows that these genes seem to be under little selective constraint compared with olfactory receptors and other genes in the studied species.
Journal ArticleDOI
Evolution of the Primate Cathelicidin CORRELATION BETWEEN STRUCTURAL VARIATIONS AND ANTIMICROBIAL ACTIVITY
Igor Zelezetsky,Alessandra Pontillo,Luca Puzzi,Nikolinka Antcheva,Ludovica Segat,Sabrina Pacor,Sergio Crovella,Alessandro Tossi +7 more
TL;DR: The evolution of cathelicidin genes homologous to the human CAMP gene, coding for the host defense peptide LL-37, have been sequenced and analyzed in 20 primate species, and two distinct types of behavior were observed.
References
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The rapid generation of mutation data matrices from protein sequences
TL;DR: An efficient means for generating mutation data matrices from large numbers of protein sequences is presented, by means of an approximate peptide-based sequence comparison algorithm, which is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fastenough to generate a matrix from a specific family or class of proteins in minutes.
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A codon-based model of nucleotide substitution for protein-coding DNA sequences.
Nick Goldman,Ziheng Yang +1 more
TL;DR: Analyses of two data sets suggest that the new codon-based model can provide a better fit to data than can nucleotide-based models and can produce more reliable estimates of certain biologically important measures such as the transition/transversion rate ratio and the synonymous/nonsynonymous substitution rate ratio.
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Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.
Ziheng Yang,Bruce Rannala +1 more
TL;DR: An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree, which has a probability of approximately 95%.
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Minimum mutation fits to a given tree
TL;DR: A method of generating all such minimum mutation fits is described, which is the assignment which permits representation of the data in a minimum number of symbols, which seems compelling in its own right.
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Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites.
Ziheng Yang,Sudhir Kumar +1 more
TL;DR: In this article, two approximate methods (one based on parsimony and one on pairwise sequence comparison) were proposed for estimating the pattern of nucleotide substitution and a parsimony-based method for estimating variable substitution rates among sites.