A model for protein sequence evolution based on selective pressure for protein stability: application to hemoglobins [0.03%]
基于选择压力的蛋白质序列进化模型（用于氧合蛋白）
Lorraine Marsh
Lorraine Marsh
Negative selection against protein instability is a central influence on evolution of proteins. Protein stability is maintained over evolution despite changes in underlying sequences. An empirical all-site stability-based model of evolution...
On the use of bootstrapped topologies in coalescent-based Bayesian MCMC inference: a comparison of estimation and computational efficiencies [0.03%]
基于靴统计拓扑的煤核基贝叶斯MCMC推理：估计与计算效率比较
Allen G Rodrigo,Peter Tsai,Helen Shearman
Allen G Rodrigo
Coalescent-based Bayesian Markov chain Monte Carlo (MCMC) inference generates estimates of evolutionary parameters and their posterior probability distributions. As the number of sequences increases, the length of time taken to complete an ...
PhyLIS: a simple GNU/Linux distribution for phylogenetics and phyloinformatics [0.03%]
PhyLIS：一个简单的GNU/Linux发行版用于系统发生和系统发育信息学
Robert C Thomson
Robert C Thomson
PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pr...
A comprehensive analysis of gene expression evolution between humans and mice [0.03%]
人类和小鼠基因表达进化全分析研究论文发表在自然杂志上
Yupeng Wang,Romdhane Rekaya
Yupeng Wang
Evolutionary changes in gene expression account for most phenotypic differences between species. Advances in microarray technology have made the systematic study of gene expression evolution possible. In this study, gene expression patterns...
A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies [0.03%]
一种混合模型和一种隐马尔可夫模型同时检测重组断点和重建系统发育树
Bastien Boussau,Laurent Guéguen,Manolo Gouy
Bastien Boussau
Homologous recombination is a pervasive biological process that affects sequences in all living organisms and viruses. In the presence of recombination, the evolutionary history of an alignment of homologous sequences cannot be properly dep...
Francisco Prosdocimi,Brandon Chisham,Enrico Pontelli et al.
Francisco Prosdocimi et al.
Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, whi...
Phylogenetic applications of the minimum contradiction approach on continuous characters [0.03%]
连续性状最小矛盾法在系统发生分析中的应用
Marc Thuillard,Didier Fraix-Burnet
Marc Thuillard
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa,...
Phylogenetic analyses reveal monophyletic origin of the ergot alkaloid gene dmaW in fungi [0.03%]
系统发育分析揭示麦角碱基因dmaW在真菌中的单系起源
Miao Liu,Daniel G Panaccione,Christopher L Schardl
Miao Liu
Ergot alkaloids are indole-derived mycotoxins that are important in agriculture and medicine. Ergot alkaloids are produced by a few representatives of two distantly related fungal lineages, the Clavicipitaceae and the Trichocomaceae. Compar...
Evolution and functional diversification of the GLI family of transcription factors in vertebrates [0.03%]
脊椎动物GLI转录因子家族的进化及功能多样化
Amir Ali Abbasi,Debbie K Goode,Saneela Amir et al.
Amir Ali Abbasi et al.
Background: In vertebrates the "SONIC HEDGEHOG" signalling pathway has been implicated in cell-fate determination, proliferation and the patterning of many different cell types and organs. As the GLI family members (GLI1,...
REFGEN and TREENAMER: automated sequence data handling for phylogenetic analysis in the genomic era [0.03%]
REFGEN和TREENAMER：基因组时代系统发育分析的自动化序列数据处理工具
Guy Leonard,Jamie R Stevens,Thomas A Richards
Guy Leonard
The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylo...