4.7 Article

POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

Patterns of Positive Selection in Seven Ant Genomes

Julien Roux et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Article Biochemistry & Molecular Biology

Selectome update: quality control and computational improvements to a database of positive selection

Sebastien Moretti et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

Comparative genomics as a tool to understand evolution and disease

Jessica Alfoeldi et al.

GENOME RESEARCH (2013)

Article Biochemistry & Molecular Biology

CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

Manuel Gil et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa

Francisco P. Lobo et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemical Research Methods

B2G-FAR, a species-centered GO annotation repository

Stefan Goetz et al.

BIOINFORMATICS (2011)

Article Evolutionary Biology

Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniae

Zhuofei Xu et al.

BMC EVOLUTIONARY BIOLOGY (2011)

Review Immunology

Mycobacterial PE/PPE Proteins at the Host-Pathogen Interface

Samantha L. Sampson

CLINICAL & DEVELOPMENTAL IMMUNOLOGY (2011)

Article Biology

Genes under positive selection in Mycobacterium tuberculosis

Yuan Zhang et al.

COMPUTATIONAL BIOLOGY AND CHEMISTRY (2011)

Article Biochemistry & Molecular Biology

PhyleasProg: a user-oriented web server for wide evolutionary analyses

Joel Busset et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Immunology

TubercuList-10 years after

Jocelyne M. Lew et al.

TUBERCULOSIS (2011)

Article Biochemical Research Methods

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

Wayne Delport et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

JCoDA: a tool for detecting evolutionary selection

Steven N. Steinway et al.

BMC BIOINFORMATICS (2010)

Review Genetics & Heredity

APPLICATIONS OF NEXT-GENERATION SEQUENCING Sequencing technologies - the next generation

Michael L. Metzker

NATURE REVIEWS GENETICS (2010)

Editorial Material Microbiology

BACTERIAL SECRETION The two faces of MycP1

Rachel David

NATURE REVIEWS MICROBIOLOGY (2010)

Article Biochemical Research Methods

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Evolutionary Biology

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment

Adrian Schneider et al.

GENOME BIOLOGY AND EVOLUTION (2009)

Article Biochemistry & Molecular Biology

Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter

Tristan Lefebure et al.

GENOME RESEARCH (2009)

Article Genetics & Heredity

Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa

Peter L. Oliver et al.

PLOS GENETICS (2009)

Article Biochemical Research Methods

IDEA: Interactive Display for Evolutionary Analyses

Amy Egan et al.

BMC BIOINFORMATICS (2008)

Article Genetics & Heredity

Patterns of Positive Selection in Six Mammalian Genomes

Carolin Kosiol et al.

PLOS GENETICS (2008)

Article Genetics & Heredity

The Population Genetics of dN/dS

Sergey Kryazhimskiy et al.

PLOS GENETICS (2008)

Article Biochemistry & Molecular Biology

Genes under positive selection in Escherichia coli

Lise Petersen et al.

GENOME RESEARCH (2007)

Article Evolutionary Biology

Phylogenomic analysis of natural selection pressure in Streptococcus genomes

Maria Anisimova et al.

BMC EVOLUTIONARY BIOLOGY (2007)

Article Biochemical Research Methods

MaxAlign: maximizing usable data in an alignment

Rodrigo Gouveia-Oliveira et al.

BMC BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach

Adi Stern et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Evolutionary Biology

Widespread positive selection in the photosynthetic Rubisco enzyme

Maxim V. Kapralov et al.

BMC EVOLUTIONARY BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites

Maria Anisimova et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

A combined empirical and mechanistic codon model

Adi Doron-Faigenboim et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biotechnology & Applied Microbiology

Evolution of the core and pan-genome of Strepococcus: positive selection, recombination, and genome composition

Tristan Lefebure et al.

GENOME BIOLOGY (2007)

Article Microbiology

Evidence for recombination in Mycobacterium tuberculosis

Xiaoming Liu et al.

JOURNAL OF BACTERIOLOGY (2006)

Article Multidisciplinary Sciences

Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli:: A comparative genomics approach

SL Chen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Multidisciplinary Sciences

An algorithm for progressive multiple alignment of sequences with insertions

A Löytynoja et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

Comparative genomics of trypanosomatid parasitic protozoa

NM El-Sayed et al.

SCIENCE (2005)

Article Biochemical Research Methods

HyPhy: hypothesis testing using phylogenies

SLK Pond et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Article Multidisciplinary Sciences

Statistical significance for genomewide studies

JD Storey et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Biochemistry & Molecular Biology

The bioperl toolkit:: Perl modules for the life sciences

JE Stajich et al.

GENOME RESEARCH (2002)

Article Biochemistry & Molecular Biology

An efficient algorithm for large-scale detection of protein families

AJ Enright et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemical Research Methods

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

HA Schmidt et al.

BIOINFORMATICS (2002)

Article Biochemistry & Molecular Biology

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution

M Anisimova et al.

MOLECULAR BIOLOGY AND EVOLUTION (2001)

Review Ecology

Statistical methods for detecting molecular adaptation

ZH Yang et al.

TRENDS IN ECOLOGY & EVOLUTION (2000)

Article Biochemistry & Molecular Biology

T-Coffee: A novel method for fast and accurate multiple sequence alignment

C Notredame et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)

Article Biochemistry & Molecular Biology

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

J Castresana

MOLECULAR BIOLOGY AND EVOLUTION (2000)