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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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Phylogenomic analysis of 11 complete African swine fever virus genome sequences
Etienne P. de Villiers,Carmina Gallardo,Marisa Arias,Melissa Da Silva,Chris Upton,Raquel Martin,Richard P. Bishop +6 more
TL;DR: Whole genome phylogenetic analysis of 123 concatenated genes from 11 ASFV genomes, including E75, a newly sequenced virulent isolate from Spain, identified two clusters, suggesting derivation from a sylvatic transmission cycle.
Journal ArticleDOI
The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host–pathogen interactions
Eric E. Smith,Harmit S. Malik +1 more
TL;DR: It is reported here that all six members of the APOL gene family present in humans have rapidly evolved in simian primates and APOL6, furthermore, shows evidence of an adaptive sweep during recent human evolution.
Journal ArticleDOI
Evolution of Coral Pigments Recreated
TL;DR: In the great star coral Montastraea cavernosa, a recreated common ancestor of green and red proteins turned out to be green, indicating that in this case red proteins evolved their color independently from most other homologous red proteins.
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Dating the Origin of the African Human T-Cell Lymphotropic Virus Type-I (HTLV-I) Subtypes
TL;DR: When the synonymous and nonsynonymous substitution ratios were compared, it was clear that purifying selection was the driving force for PTLV-I evolution in the env gene, irrespective of the host species.
Posted ContentDOI
Host and infectivity prediction of Wuhan 2019 novel coronavirus using deep learning algorithm
Qian Guo,Mo Li,Chunhui Wang,Zhengcheng Fang,Peihong Wang,Jie Tan,Shufang Wu,Yonghong Xiao,Huaiqiu Zhu +8 more
TL;DR: The VHP (Virus Host Prediction) was introduced to predict the potential hosts of viruses using deep learning algorithm and demonstrated that several vertebrate-infectious coronaviruses have strong potential to infect human.
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.