4.8 Article

INDELible: A Flexible Simulator of Biological Sequence Evolution

Related references

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

Problems and Solutions for Estimating Indel Rates and Length Distributions

Reed A. Cartwright

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Review Biochemistry & Molecular Biology

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

Maria Anisimova et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Article Biochemistry & Molecular Biology

Simulating DNA coding sequence evolution with EvolveAGene 3

Barry G. Hall

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Biochemistry & Molecular Biology

An improved general amino acid replacement matrix

Si Quang Le et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Biotechnology & Applied Microbiology

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

Avinash Varadarajan et al.

GENOME BIOLOGY (2008)

Article Biochemistry & Molecular Biology

An empirical codon model for protein sequence evolution

Carolin Kosiol et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Multidisciplinary Sciences

HIV-Specific Probabilistic Models of Protein Evolution

David C. Nickle et al.

PLOS ONE (2007)

Article Biochemistry & Molecular Biology

Indel-Seq-Gen: A new protein family simulator incorporating domains, motifs, and indels

Cory L. Strope et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution

Samuel Blanquart et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Biochemistry & Molecular Biology

An initial map of insertion and deletion (INDEL) variation in the human genome

Ryan E. Mills et al.

GENOME RESEARCH (2006)

Article Biochemistry & Molecular Biology

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level

JZ Zhang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Biochemistry & Molecular Biology

Bayes empirical Bayes inference of amino acid sites under positive selection

ZH Yang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Biochemical Research Methods

DNA assembly with gaps (Dawg): simulating sequence evolution

RA Cartwright

BIOINFORMATICS (2005)

Article Evolutionary Biology

The importance of proper model assumption in Bayesian phylogenetics

AR Lemmon et al.

SYSTEMATIC BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Indel-based evolutionary distance and mouse-human divergence

AY Ogurtsov et al.

GENOME RESEARCH (2004)

Article Biochemistry & Molecular Biology

Reconstructing large regions of an ancestral mammalian genome in silico

M Blanchette et al.

GENOME RESEARCH (2004)

Article Biochemical Research Methods

Regional and time-resolved mutation patterns of the human genome

PF Arndt et al.

BIOINFORMATICS (2004)

Article Multidisciplinary Sciences

Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes

WJ Kent et al.

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

Article Biochemistry & Molecular Biology

Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes

ZL Zhang et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Multidisciplinary Sciences

Majority of divergence between closely related DNA samples is due to indels

RJ Britten et al.

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

Review Multidisciplinary Sciences

Initial sequencing and comparative analysis of the mouse genome

RH Waterston et al.

NATURE (2002)

Article Genetics & Heredity

Patterns in spontaneous mutation revealed by human-baboon sequence comparison

JC Silva et al.

TRENDS IN GENETICS (2002)

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

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages

ZH Yang et al.

MOLECULAR BIOLOGY AND EVOLUTION (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

Modeling amino acid replacement

T Muller et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2000)