ALF—A Simulation Framework for Genome Evolution

OrthoInspector: comprehensive orthology analysis and visual exploration

(2011) Benjamin Linard et al.   BMC BIOINFORMATICS

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

(2011) Botond Sipos et al.   BMC BIOINFORMATICS

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

(2011) B. Boeckmann et al.   BRIEFINGS IN BIOINFORMATICS

Simulating Sequences of the Human Genome with Rare Variants

(2011) Bo Peng et al.   HUMAN HEREDITY

Markov Models of Amino Acid Substitution to Study Proteins with Intrinsically Disordered Regions

(2011) Adam M. Szalkowski et al.   PLoS One

TreesimJ: a flexible, forward time population genetic simulator

(2010) B. O'Fallon   BIOINFORMATICS

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lateral genetic transfer: open issues

(2009) M. A. Ragan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

A flexible forward simulator for populations subject to selection and demography

(2008) R. D. Hernandez   BIOINFORMATICS

Fregene: Simulation of realistic sequence-level data in populations and ascertained samples

(2008) Marc Chadeau-Hyam et al.   BMC BIOINFORMATICS

Algorithm of OMA for large-scale orthology inference

(2008) Alexander CJ Roth et al.   BMC BIOINFORMATICS

Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise

(2008) Christophe Dessimoz et al.   BMC EVOLUTIONARY BIOLOGY

Evolution of protein domain promiscuity in eukaryotes

(2008) M. K. Basu et al.   GENOME RESEARCH

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

(2008) M. Anisimova et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simulating DNA Coding Sequence Evolution with EvolveAGene 3

(2008) B. G. Hall   MOLECULAR BIOLOGY AND EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION