4.8 Article

An improved general amino acid replacement matrix

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

An empirical codon model for protein sequence evolution

Carolin Kosiol et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemical Research Methods

XRate:: a fast prototyping, training and annotation tool for phylo-grammars

Peter S. Klosterman et al.

BMC BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

Efficient methods for estimating amino acid replacement rates

Lars Arvestad

JOURNAL OF MOLECULAR EVOLUTION (2006)

Article Biochemistry & Molecular Biology

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

N Lartillot et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Evolutionary Biology

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood

S Guindon et al.

SYSTEMATIC BIOLOGY (2003)

Article Biochemistry & Molecular Biology

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

B Boeckmann et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemical Research Methods

A transition probability model for amino acid substitutions from blocks

S Veerassamy et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2003)

Article Biochemistry & Molecular Biology

rtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny

MW Dimmic et al.

JOURNAL OF MOLECULAR EVOLUTION (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

The Pfam Protein Families Database

A Bateman et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemistry & Molecular Biology

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

S Whelan et al.

MOLECULAR BIOLOGY AND EVOLUTION (2001)

Article Biochemical Research Methods

Rate matrices for analyzing large families of protein sequences

C Devauchelle et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2001)

Article Cell Biology

Models of protein sequence evolution and their applications

JL Thorne

CURRENT OPINION IN GENETICS & DEVELOPMENT (2000)

Article Evolutionary Biology

Likelihood-based tests of topologies in phylogenetics

N Goldman et al.

SYSTEMATIC 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)

Article Biochemical Research Methods

Modeling amino acid replacement

T Muller et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2000)