Minimum conflict individual haplotyping from SNP fragments and related genotype [0.03%]
基于基因型和SNP片段的最小冲突单倍型重建问题
Xiang-Sun Zhang,Rui-Sheng Wang,Ling-Yun Wu et al.
Xiang-Sun Zhang et al.
The Minimum Error Correction (MEC) is an important model for haplotype reconstruction from SNP fragments. However, this model is effective only when the error rate of SNP fragments is low. In this paper, we propose a new computational model...
Andrew D Fernandes,William R Atchley
Andrew D Fernandes
We present computational methods and subroutines to compute Gaussian quadrature integration formulas for arbitrary positive measures. For expensive integrands that can be factored into well-known forms, Gaussian quadrature schemes allow for...
LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies [0.03%]
激光：一种从分子谱系树中检测分化率时间变化的极大似然工具包
Daniel L Rabosky
Daniel L Rabosky
Rates of species origination and extinction can vary over time during evolutionary radiations, and it is possible to reconstruct the history of diversification using molecular phylogenies of extant taxa only. Maximum likelihood methods prov...
A new effective method for estimating missing values in the sequence data prior to phylogenetic analysis [0.03%]
一种在系统发生分析前用于序列数据估算缺失值的新有效方法
Abdoulaye Baniré Diallo,François-Joseph Lapointe,Vladimir Makarenkov
Abdoulaye Baniré Diallo
In this article we address the problem of phylogenetic inference from nucleic acid data containing missing bases. We introduce a new effective approach, called "Probabilistic estimation of missing values" (PEMV), allowing one to estimate un...
Estimating population parameters using the structured serial coalescent with Bayesian MCMC inference when some demes are hidden [0.03%]
利用结构化序列共轭和贝叶斯MCMC进行种群参数估计及其在部分隐秘族群中的应用
Greg Ewing,Allen Rodrigo
Greg Ewing
Using the structured serial coalescent with Bayesian MCMC and serial samples, we estimate population size when some demes are not sampled or are hidden, ie ghost demes. It is found that even with the presence of a ghost deme, accurate infer...
Unravelling selection shifts among foot-and-mouth disease virus (FMDV) serotypes [0.03%]
口蹄疫病毒各血清型的选择压力变化分析
Damien C Tully,Mario A Fares
Damien C Tully
FMDV virus has been increasingly recognised as the most economically severe animal virus with a remarkable degree of antigenic diversity. Using an integrative evolutionary and computational approach we have compelling evidence for heterogen...
Spectral analysis of sequence variability in basic-helix-loop-helix (bHLH) protein domains [0.03%]
基本螺旋环螺旋结构域的序列多态性分析
Zhi Wang,William R Atchley
Zhi Wang
The basic helix-loop-helix (bHLH) family of transcription factors is used as a paradigm to explore structural implications of periodicity patterns in amino acid sequence variability. A Boltzmann-Shannon entropy profile represents site-by-si...
PIRSF family classification system for protein functional and evolutionary analysis [0.03%]
蛋白质功能和进化分析的PIRSF族分类体系
Anastasia N Nikolskaya,Cecilia N Arighi,Hongzhan Huang et al.
Anastasia N Nikolskaya et al.
The PIRSF protein classification system (http://pir.georgetown.edu/pirsf/) reflects evolutionary relationships of full-length proteins and domains. The primary PIRSF classification unit is the homeomorphic family, whose members are both hom...
CoMET: a Mesquite package for comparing models of continuous character evolution on phylogenies [0.03%]
CoMET：一个在系统树中比较连续特征演化模型的Mesquite程序包
Chunghau Lee,Sigal Blay,Arne Ø Mooers et al.
Chunghau Lee et al.
Continuously varying traits such as body size or gene expression level evolve during the history of species or gene lineages. To test hypotheses about the evolution of such traits, the maximum likelihood (ML) method is often used. Here we i...
MBEToolbox 2.0: an enhanced version of a MATLAB toolbox for molecular biology and evolution [0.03%]
MBEToolbox 2.0：分子生物学和演化的MATLAB工具箱增强版
James J Cai,David K Smith,Xuhua Xia et al.
James J Cai et al.
MBEToolbox is an extensible MATLAB-based software package for analysis of DNA and protein sequences. MBEToolbox version 2.0 includes enhanced functions for phylogenetic analyses by the maximum likelihood method. For example, it is capable o...