4.8 Article

Learning to Count: Robust Estimates for Labeled Distances between Molecular Sequences

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

Zachary D. Blount et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biology

Counting labeled transitions in continuous-time Markov models of evolution

Vladimir N. Minin et al.

JOURNAL OF MATHEMATICAL BIOLOGY (2008)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

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 Biochemical Research Methods

Tree and rate estimation by local evaluation of heterochronous nucleotide data

Zhu Yang et al.

BIOINFORMATICS (2007)

Article Biochemical Research Methods

Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human

Leo Goodstadt et al.

PLOS COMPUTATIONAL BIOLOGY (2006)

Article Biochemical Research Methods

The Jalview Java alignment editor

M Clamp et al.

BIOINFORMATICS (2004)

Article Biochemical Research Methods

ClustalW-MPI: ClustalW analysis using distributed and parallel computing

KB Li

BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

R Wernersson et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Multidisciplinary Sciences

Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus

JB Plotkin et al.

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

Article Multidisciplinary Sciences

Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus

JB Plotkin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemistry & Molecular Biology

An expectation maximization algorithm for training hidden substitution models

I Holmes et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Article Biochemistry & Molecular Biology

Bayesian selection of continuous-time Markov chain evolutionary models

MA Suchard et al.

MOLECULAR BIOLOGY AND EVOLUTION (2001)

Article Biochemistry & Molecular Biology

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

ZH Yang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2000)