MODELTEST: testing the model of DNA substitution. - David Posada; Keith A. Crandall (Bioinform., 1998)

TCS: Estimating Gene Genealogies. - Mark J. Clement; Quinn Snell; Peter Walker; David Posada; Keith A. Crandall (IPDPS, 2002)

Simulating haplotype blocks in the human genome. - David Posada; Carsten Wiuf (Bioinform., 2003)

ProtTest: selection of best-fit models of protein evolution. - Federico Abascal; Rafael Zardoya; David Posada (Bioinform., 2005)

RDP2: recombination detection and analysis from sequence alignments. - Darren P. Martin; Carolyn Williamson; David Posada (Bioinform., 2005)

TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees. - David Posada; Taylor J. Maxwell; Alan R. Templeton (Bioinform., 2005)

GARD: a genetic algorithm for recombination detection. - Sergei L. Kosakovsky Pond; David Posada; Michael B. Gravenor; Christopher H. Woelk; Simon D. W. Frost (Bioinform., 2006)

GenDecoder: genetic code prediction for metazoan mitochondria. - Federico Abascal; Rafael Zardoya; David Posada (Nucleic Acids Res., 2006)

ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. - David Posada (Nucleic Acids Res., 2006)

Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. - Miguel Arenas; David Posada (BMC Bioinform., 2007)

Automatic Prediction of the Genetic Code. - Mateus Patricio; Jaime Huerta-Cepas; Toni Gabaldón; Rafael Zardoya; David Posada (IWANN (2), 2009)

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1. - Sergei L. Kosakovsky Pond; David Posada; Eric W. Stawiski; Colombe Chappey; Art F. Y. Poon; Gareth Hughes; Esther Fearnhill; Mike B. Gravenor; Andrew J. Leigh Brown; Simon D. W. Frost (PLoS Comput. Biol., 2009)

ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution. - Diego Darriba; Guillermo L. Taboada; Ramon Doallo; David Posada (Euro-Par Workshops, 2010)

Grid selection of models of nucleotide substitution. - Marta Loureiro; Miguel Pan; Manuel Aurelio Rodriguez Pascual; David Posada; Rafael Mayo 001 (HealthGrid, 2010)

Accurate Selection of Models of Protein Evolution. - Mateus Patricio; Federico Abascal; Rafael Zardoya; David Posada (IWPACBB, 2010)

RDP3: a flexible and fast computer program for analyzing recombination. - Darren P. Martin; Philippe Lemey; Martin Lott; Vincent Moulton; David Posada; Pierre Lefeuvre (Bioinform., 2010)

Characterization of phylogenetic networks with NetTest. - Miguel Arenas; Mateus Patricio; David Posada; Gabriel Valiente (BMC Bioinform., 2010)

ALTER: program-oriented conversion of DNA and protein alignments. - Daniel Glez-Peña; Daniel Gómez-Blanco; Miguel Reboiro-Jato; Florentino Fdez-Riverola; David Posada (Nucleic Acids Res., 2010)

HPC selection of models of DNA substitution. - Diego Darriba; Guillermo L. Taboada; Ramon Doallo; David Posada (CMSB, 2011)

ProtTest 3: fast selection of best-fit models of protein evolution. - Diego Darriba; Guillermo L. Taboada; Ramon Doallo; David Posada (Bioinform., 2011)

Protein evolution along phylogenetic histories under structurally constrained substitution models. - Miguel Arenas; Helena G. Dos Santos; David Posada; Ugo Bastolla (Bioinform., 2013)

jmodeltest.org: selection of nucleotide substitution models on the cloud. - Jose Manuel Santorum; Diego Darriba; Guillermo L. Taboada; David Posada (Bioinform., 2014)

High-performance computing selection of models of DNA substitution for multicore clusters. - Diego Darriba; Guillermo L. Taboada; Ramon Doallo; David Posada (Int. J. High Perform. Comput. Appl., 2014)

Adapting Reproducible Research Capabilities to Resilient Distributed Calculations. - Manuel Aurelio Rodriguez Pascual; Christos Kanellopoulos; Antonio J. Rubio-Montero; Diego Darriba; Ognjen Prnjat; David Posada; Rafael Mayo-García (Int. J. Grid High Perform. Comput., 2016)

RecPhyloXML: a format for reconciled gene trees. - Wandrille Duchemin; Guillaume Gence; Anne-Muriel Arigon Chifolleau; Lars Arvestad; Mukul S. Bansal; Vincent Berry; Bastien Boussau; François Chevenet; Nicolas Comte; Adrián A. Davín; Christophe Dessimoz; David Dylus; et al. (Bioinform., 2018)

NGSphy: phylogenomic simulation of next-generation sequencing data. - Merly Escalona; Sara Rocha; David Posada (Bioinform., 2018)

Exploring the Solution Space of Cancer Evolution Inference Frameworks for Single-Cell Sequencing Data. - Davide Maspero; Fabrizio Angaroni; Lucrezia Patruno; Daniele Ramazzotti; David Posada; Alex Graudenzi (WIVACE, 2022)

Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data. - Mohammad Amin Edrisi; Monica V. Valecha; Sunkara B. V. Chowdary; Sergio Robledo; Huw A. Ogilvie; David Posada; Hamim Zafar; Luay Nakhleh (Bioinform., 2022)