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。GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
Guangchuang Yu et al.
METHODS IN ECOLOGY AND EVOLUTION (2017)
From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing
Marion Cornelissen et al.
VIRUS RESEARCH (2017)
RECONSTRUCTING TRANSMISSION TREES FOR COMMUNICABLE DISEASES USING DENSELY SAMPLED GENETIC DATA
Colin J. Worby et al.
ANNALS OF APPLIED STATISTICS (2016)
Coming of age: ten years of next-generation sequencing technologies
Sara Goodwin et al.
NATURE REVIEWS GENETICS (2016)
Phylogenetically resolving epidemiologic linkage
Ethan O. Romero-Severson et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict
Nicholas J. Croucher et al.
PLOS BIOLOGY (2016)
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
Andrew Rambaut et al.
VIRUS EVOLUTION (2016)
IVA: accurate de novo assembly of RNA virus genomes
Martin Hunt et al.
BIOINFORMATICS (2015)
Efficacy of Sofosbuvir Plus Ribavirin With or Without Peginterferon-Alfa in Patients With Hepatitis C Virus Genotype 3 Infection and Treatment-Experienced Patients With Cirrhosis and Hepatitis C Virus Genotype 2 Infection
Graham R. Foster et al.
GASTROENTEROLOGY (2015)
Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set
Matthew Hall et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Population genomics of intrapatient HIV-1 evolution
Fabio Zanini et al.
ELIFE (2015)
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Nicholas J. Croucher et al.
NUCLEIC ACIDS RESEARCH (2015)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Alexandros Stamatakis
BIOINFORMATICS (2014)
HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model
Sandhya Prabhakaran et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2014)
Two-phase importance sampling for inference about transmission trees
Elina Numminen et al.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2014)
Virulence and Pathogenesis of HIV-1 Infection: An Evolutionary Perspective
Christophe Fraser et al.
SCIENCE (2014)
Viral Quasispecies Assembly via Maximal Clique Enumeration
Armin Toepfer et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Thibaut Jombart et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Complete Genome Sequence of the WHO International Standard for HIV-1 RNA Determined by Deep Sequencing
Astrid Gall et al.
GENOME ANNOUNCEMENTS (2014)
Inferring the Source of Transmission with Phylogenetic Data
Erik M. Volz et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
HIV-1 Dual Infection Is Associated With Faster CD4+ T-Cell Decline in a Cohort of Men With Primary HIV Infection
Marion Cornelissen et al.
CLINICAL INFECTIOUS DISEASES (2012)
Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes
Astrid Gall et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2012)
Optimal enzymes for amplifying sequencing libraries
Michael A. Quail et al.
NATURE METHODS (2012)
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Fredrik Ronquist et al.
SYSTEMATIC BIOLOGY (2012)
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data
Osvaldo Zagordi et al.
BMC BIOINFORMATICS (2011)
Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID
Cassandra B. Jabara et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Morgan N. Price et al.
MOLECULAR BIOLOGY AND EVOLUTION (2009)
A large genome center's improvements to the Illumina sequencing system
Michael A. Quail et al.
NATURE METHODS (2008)
The Los Alamos hepatitis C sequence database
C Kuiken et al.
BIOINFORMATICS (2005)
Cytoscape: A software environment for integrated models of biomolecular interaction networks
P Shannon et al.
GENOME RESEARCH (2003)
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
K Katoh et al.
NUCLEIC ACIDS RESEARCH (2002)
Amino acid substitutions in Gag protein at non-cleavage sites are indispensable for the development of a high multitude of HIV-1 resistance against protease inhibitors
H Gatanaga et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2002)