Phylogenetic Inferences from Molecular Sequences: Review and Critique

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

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

1987 • 59,130 citations

Evolutionary trees from DNA sequences: A maximum likelihood approach

1981 • 14,097 citations

A general method applicable to the search for similarities in the amino acid sequence of two proteins

1970 • 11,049 citations

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

2000 • 9,575 citations

The Neutral Theory of Molecular Evolution

1979 • 7,965 citations

The Jackknife, the Bootstrap and Other Resampling Plans

1982 • 7,816 citations

Amino acid substitution matrices from protein blocks.

1992 • 5,998 citations

Fitting a mixture model by expectation maximization to discover motifs in biopolymers.

1994 • 4,818 citations

Atlas of protein sequence and structure

1965 • 4,462 citations

An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis

1993 • 3,388 citations

Cases in which Parsimony or Compatibility Methods will be Positively Misleading

1978 • 2,881 citations

The Jackknife: The Bootstrap and Other Resampling Plans.

1983 • 2,827 citations

Atlas of Protein Sequence and Structure, 1972.

1973 • 2,408 citations

Bacterial evolution

1987 • 2,303 citations

Cases in which Parsimony or Compatibility Methods Will be Positively Misleading

1978 • 2,193 citations

PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITY

1988 • 2,143 citations

Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment

1993 • 1,835 citations

Mitochondrial Evolution

1999 • 1,603 citations

Distinguishing Homologous from Analogous Proteins

1970 • 1,512 citations

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

1999 • 1,505 citations

The neutral theory of molecular evolution

1984 • 1,459 citations

The Phylogeny of Prokaryotes

1980 • 1,457 citations

Signal, Noise, and Reliability in Molecular Phylogenetic Analyses

1992 • 1,329 citations

Molecules as documents of evolutionary history

1965 • 1,305 citations

The hydrogen hypothesis for the first eukaryote

1998 • 1,240 citations

Horizontal gene transfer among genomes: The complexity hypothesis

1999 • 1,173 citations

Phylogeny Estimation and Hypothesis Testing Using Maximum Likelihood

1997 • 1,076 citations

The universal ancestor

1998 • 1,033 citations

A workbench for multiple alignment construction and analysis

1991 • 1,005 citations

Molecular archaeology of the Escherichia coli genome

1998 • 937 citations

A Framework for the Quantitative Study of Evolutionary Trees

1989 • 833 citations

Bootstrap confidence levels for phylogenetic trees.

1996 • 708 citations

Dinucleotide relative abundance extremes: a genomic signature

1995 • 681 citations

You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes

1998 • 607 citations

Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes

1998 • 599 citations

Horizontal gene transfer and the origin of species: lessons from bacteria

2000 • 556 citations

Genomic evidence for two functionally distinct gene classes

1998 • 542 citations

Phylogenetic analysis Of Dna sequences

1991 • 521 citations

COULD A CLADOGRAM THIS SHORT HAVE ARISEN BY CHANCE ALONE?: ON PERMUTATION TESTS FOR CLADISTIC STRUCTURE

1991 • 508 citations

Measuring genome evolution

1998 • 449 citations

Compositional biases of bacterial genomes and evolutionary implications

1997 • 445 citations

Archaea and the prokaryote-to-eukaryote transition

1997 • 440 citations

A Randomization Test for Phylogenetic Information in Systematic Data

1989 • 377 citations

Convergent evolution: the need to be explicit

1994 • 367 citations

Proceedings: Second international conference on intelligent systems for molecular biology

1994 • 349 citations

Evidence that eukaryotes and eocyte prokaryotes are immediate relatives

1992 • 339 citations

PHYLOGENETIC ANALYSIS IN MOLECULAR EVOLUTIONARY GENETICS

1996 • 336 citations

Discriminating Between Phylogenetic Signal and Random Noise in DNA Sequences

1991 • 325 citations

How good are deep phylogenetic trees?

1998 • 324 citations

The Retention Index and Homoplasy Excess

1989 • 323 citations

Phylogenetic analysis using parsimony and likelihood methods

1996 • 317 citations

Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea

1997 • 316 citations

Symbiosis Between Methanogenic Archaea and δ-Proteobacteria as the Origin of Eukaryotes: The Syntrophic Hypothesis

1998 • 313 citations

Whole genome-based phylogenetic analysis of free-living microorganisms

1999 • 306 citations

Pattern-induced multi-sequence alignment (PUMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling

1992 • 281 citations

Fitting Discrete Probability Distributions to Evolutionary Events

1971 • 277 citations

Archaea and the prokaryote-to-eukaryote transition.

1997 • 272 citations

The Rooting of the Universal Tree of Life Is Not Reliable

1999 • 264 citations

Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA

1999 • 259 citations

Compositional differences within and between eukaryotic genomes

1997 • 255 citations

Metabolic symbiosis at the origin of eukaryotes

1999 • 245 citations

Sequence-dependent DNA structure: tetranucleotide conformational maps

2000 • 241 citations

The origin of the eukaryotic cell.

1996 • 238 citations

Tree-Length Distribution Skewness: An Indicator of Phylogenetic Information

1991 • 229 citations

On global sequence alignment

1994 • 229 citations

Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.

1996 • 224 citations

Global dinucleotide signatures and analysis of genomic heterogeneity

1998 • 216 citations

Homoplasy Excess Ratios: New Indices for Measuring Levels of Homoplasy in Phylogenetic Systematics and a Critique of the Consistency Index

1989 • 210 citations

The origin of the eukaryotic cell

1996 • 204 citations

HOMOPLASY AND THE CHOICE AMONG CLADOGRAMS

1991 • 200 citations

Conservation among HSP60 sequences in relation to structure, function, and evolution

2000 • 177 citations

Sequence-dependent DNA structure: dinucleotide conformational maps

2000 • 138 citations

The Root of the Tree of Life in the Light of the Covarion Model

1999 • 136 citations

RecA-like Recombination Proteins in Eukaryotes: Functions and Structures of RAD51 Genes

1993 • 118 citations

Problems with Parsimony in Sequences of Biased Base Composition

1998 • 113 citations

The consistency of several phylogeny-inference methods under varying evolutionary rates.

1992 • 107 citations

Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites

1995 • 105 citations

Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated.

1989 • 97 citations

Consistency, Characters, and the Likelihood of Correct Phylogenetic Inference

1997 • 96 citations

Archaeal genomics: Do archaea have a mixed heritage?

1998 • 94 citations

Similarities and dissimilarities of phage genomes.

1996 • 93 citations

Escaping from the Felsenstein Zone by Detecting Long Branches in Phylogenetic Data

1997 • 91 citations

Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites

1994 • 87 citations

Statistical Methods and Insights for Protein and DNA Sequences

1991 • 85 citations

Evolution of microbial life

1996 • 82 citations

Is There a Phylogenetic Signal in Prokaryote Proteins?

1999 • 82 citations

Measuring Residue Association in Protein Structures Possible Implications for Protein Folding

1994 • 82 citations

A stepwise algorithm for finding minimum evolution trees

1996 • 81 citations

Evolutionary anomalies among the aminoacyl-tRNA synthetases

1998 • 80 citations

Evolution of microbial life

1997 • 79 citations

Heat shock protein 60 sequence comparisons: Duplications, lateral transfer, and mitochondrial evolution

2000 • 79 citations

A symmetric-iterated multiple alignment of protein sequences

1998 • 67 citations

Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models

1999 • 66 citations

Discovering structural correlations in α‐helices

1994 • 65 citations

New insights into the phylogeny of eukaryotes based on ciliate Hsp70 sequences

1998 • 59 citations

Homoplasy Slope Ratio: A Better Measurement of Observed Homoplasy in Cladistic Analyses

1991 • 58 citations

Generalized neighbor-joining: more reliable phylogenetic tree reconstruction

1999 • 52 citations

Expression of recA in Deinococcus radiodurans

1996 • 51 citations

Lateral Gene Transfer in Prokaryotes

2000 • 49 citations

A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes

1999 • 48 citations

Horizontal transfer of catalase-peroxidase genes between Archaea and pathogenic bacteria

2000 • 45 citations

Homoplasy Slope Ratio: A Better Measurement of Observed Homoplasy in Cladistic Analyses

1991 • 41 citations

Significant similarity and dissimilarity in homologous proteins.

1992 • 29 citations

Engineering of bacterial ribosomes: Replacement of all seven Escherichia coli rRNA operons by a single plasmid-encoded operon

1999 • 28 citations

Optimally recovering rate variation information from genomes and sequences: pattern filtering

1998 • 20 citations

Branch Length Heterogeneity Leads to Nonindependent Branch Length Estimates and Can Decrease the Efficiency of Methods of Phylogenetic Inference

1999 • 15 citations

A Novel Approach to Phylogeny Reconstruction from Protein Sequences

1999 • 7 citations

Deleted Work

1955 • 0 citations