From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

1994 • 63,397 citations

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

2007 • 29,037 citations

PHYLIP-Phylogeny inference package (Version 3.2)

1989 • 17,674 citations

The Complete Genome Sequence of Escherichia coli K-12

1997 • 7,325 citations

The rapid generation of mutation data matrices from protein sequences

1992 • 6,766 citations

Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd

1995 • 5,571 citations

Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen

2000 • 4,351 citations

Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference

1999 • 4,194 citations

Lateral gene transfer and the nature of bacterial innovation

2000 • 3,715 citations

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

2002 • 2,565 citations

Bacterial evolution.

1987 • 2,521 citations

Bacterial evolution

1987 • 2,303 citations

SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny

1996 • 2,249 citations

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7

2001 • 2,017 citations

Phylogenetic Classification and the Universal Tree

1999 • 1,872 citations

DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae

2000 • 1,833 citations

Complete genome sequence of Salmonella enterica serovar Typhimurium LT2

2001 • 1,829 citations

Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

1999 • 1,505 citations

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18

2001 • 1,277 citations

Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS

2000 • 1,248 citations

Genome sequence of Yersinia pestis, the causative agent of plague

2001 • 1,213 citations

Comparison of the genomes of two Xanthomonas pathogens with differing host specificities

2002 • 1,201 citations

Horizontal gene transfer among genomes: The complexity hypothesis

1999 • 1,173 citations

Likelihood-Based Tests of Topologies in Phylogenetics

2000 • 1,138 citations

MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers

1994 • 1,092 citations

Accelerated evolution and Muller's rachet in endosymbiotic bacteria.

1996 • 983 citations

Prokaryotic Evolution in Light of Gene Transfer

2002 • 965 citations

The genome sequence of the plant pathogen Xylella fastidiosa

2000 • 928 citations

Increased Taxon Sampling Greatly Reduces Phylogenetic Error

2002 • 924 citations

Amelioration of Bacterial Genomes: Rates of Change and Exchange

1997 • 848 citations

Origins of Highly Mosaic Mycobacteriophage Genomes

2003 • 652 citations

Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia

2002 • 603 citations

Genome Sequence of Yersinia pestis KIM

2002 • 539 citations

GenBank

2002 • 447 citations

Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses

2002 • 402 citations

Universal trees based on large combined protein sequence data sets

2001 • 391 citations

Histidine protein kinases: key signal transducers outside the animal kingdom.

2002 • 364 citations

Genome trees and the tree of life

2002 • 362 citations

Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?

2003 • 353 citations

Complete genomic sequence of Pasteurella multocida ,Pm70

2001 • 340 citations

Phylogenetics and the Cohesion of Bacterial Genomes

2003 • 299 citations

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli

1996 • 295 citations

Ancient horizontal gene transfer

2003 • 285 citations

Distinct Types of rRNA Operons Exist in the Genome of the Actinomycete Thermomonospora chromogena and Evidence for Horizontal Transfer of an Entire rRNA Operon

1999 • 271 citations

Nucleotide Bias Causes a Genomewide Bias in the Amino Acid Composition of Proteins

2000 • 269 citations

The process of genome shrinkage in the obligate symbiont Buchnera aphidicola

2001 • 266 citations

Sequence evolution in bacterial endosymbionts having extreme base compositions

1999 • 199 citations

The source of laterally transferred genes in bacterial genomes

2003 • 177 citations

Evolutionary dynamics of full genome content in Escherichia coli

2000 • 166 citations

Two Distinct Mechanisms Cause Heterogeneity of 16S rRNA

1999 • 158 citations

Eubacterial phylogeny based on translational apparatus proteins

2002 • 156 citations

A Comparative Analysis of ABC Transporters in Complete Microbial Genomes

1998 • 140 citations

The evolutionary history of ribosomal protein RpS14:

2000 • 127 citations

Phylogenetic Characterization and Molecular Evolution of Bacterial Endosymbionts in Psyllids (Hemiptera: Sternorrhyncha)

1998 • 83 citations

Defining the Core of Nontransferable Prokaryotic Genes: The Euryarchaeal Core

2001 • 76 citations

Putative evolutionary origin of plasmids carrying the genes involved in leucine biosynthesis in Buchnera aphidicola (endosymbiont of aphids)

1997 • 67 citations

Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylellaspecies and in heterocystous cyanobacteria

2003 • 30 citations

Comparative Molecular Evolution of Primary (Buchnera) and Secondary Symbionts of Aphids Based on Two Protein-Coding Genes

2002 • 25 citations

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