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List of works by David Posada

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

scientific article (publication date: May 2016)

A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis

scientific article

A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints

scholarly article by D.P. Martin published in January 2005

A coalescent model of recombination hotspots

scientific article

A comparison of phylogenetic network methods using computer simulation

scientific article

A comparison of tools for the simulation of genomic next-generation sequencing data

scientific article

ALTER: program-oriented conversion of DNA and protein alignments

scientific article published on 3 May 2010

Accurate Selection of Models of Protein Evolution

Advances in understanding the evolution of HIV.

scientific article published in January 1999

An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1

scientific article

An exact nonparametric method for inferring mosaic structure in sequence triplets

scientific article published on 3 April 2007

Analysing recombination in nucleotide sequences

scientific article published on 19 May 2011

Are the sexual, somatic and genetic characters enough to solve nomenclatural problems in lumbricid taxonomy?

Author Correction: A comparison of tools for the simulation of genomic next-generation sequencing data

scientific article published on 01 November 2018

Automated phylogenetic detection of recombination using a genetic algorithm

scientific article published on 3 July 2006

Automatic Prediction of the Genetic Code

Base-Pairing Versatility Determines Wobble Sites in tRNA Anticodons of Vertebrate Mitogenomes ⬇️

scientific article published on May 9, 2012

Bioinformatics for DNA Sequence Analysis

article

Cancer Molecular Evolution

scientific article published on 20 August 2015

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data

scientific article published on 26 January 2022

Characterization of Reticulate Networks Based on the Coalescent with Recombination

scientific article published in 2009

Characterization of phylogenetic networks with NetTest

scientific article

Characterization of reticulate networks based on the coalescent with recombination

scientific article

Coalescent simulation of intracodon recombination

scientific article

CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation

scientific article published on 9 January 2015

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation

scientific article published on 23 October 2013

Computational Design of Centralized HIV-1 Genes ⬇️

scientific article published on December 1, 2010

Correction: A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis

scientific article published on 21 July 2016

Cryptic diversity within the endemic prehensile-tailed geckoUrocotyledon inexpectataacross the Seychelles Islands: patterns of phylogeographical structure and isolation at the multilocus level

Disease progression and evolution of the HIV-1 env gene in 24 infected infants

scientific article published in November 2007

Effective population sizes: missing measures and missing concepts

article published in 1999

Effective population sizes: missing measures and missing concepts

Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial

scientific article

Evaluation of methods for detecting recombination from DNA sequences: Computer simulations ⬇️

scientific article published on November 20, 2001

Evaluation of methods for detecting recombination from DNA sequences: empirical data

scientific article

Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soós 1926) (Helicellinae, Stylommatophora)

scientific article

Evolutionary history ofTrachylepisskinks in the Seychelles islands: introgressive hybridization, morphological evolution and geographic structure

GARD: a genetic algorithm for recombination detection

scientific article published on 16 November 2006

GenDecoder: genetic code prediction for metazoan mitochondria

scientific article

Gene expression analysis of clams Ruditapes philippinarum and Ruditapes decussatus following bacterial infection yields molecular insights into pathogen resistance and immunity

scientific article

Genetic Identification of the Northeastern Atlantic Spiny Spider Crab as Maja Brachydactyla Balss, 1922

scientific article published in 2008

Genetic code prediction for metazoan mitochondria with GenDecoder

scientific article published in January 2009

Genetic variation at MHC, mitochondrial and microsatellite loci in isolated populations of Brown trout (Salmo trutta)

Genetic variation of the spiny spider crab Maja brachydactyla in the northeastern Atlantic

article published in 2008

Genome-wide heterogeneity of nucleotide substitution model fit.

scientific article published on 07 August 2011

GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes

article

Grid selection of models of nucleotide substitution.

scientific article published on January 2010

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations

scientific article

HIV-1 infected monozygotic twins: a tale of two outcomes

scientific article

HPC selection of models of DNA substitution

article

High-performance computing selection of models of DNA substitution for multicore clusters

How does recombination affect phylogeny estimation?

scientific article published on 01 December 2000

Identification and characterization of microsatellite loci in the spiny spider crab Maja brachydactyla

Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba

scientific article published on June 2007

Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in Cuba

scientific article

Individual sequence variability and functional activities of fibrinogen-related proteins (FREPs) in the Mediterranean mussel (Mytilus galloprovincialis) suggest ancient and complex immune recognition models in invertebrates

scientific article published on 19 November 2010

Infinitely Long Branches and an Informal Test of Common Ancestry

Infinitely long branches and an informal test of common ancestry

scientific article

Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada

scientific article published on 13 August 2012

Intraspecific gene genealogies: trees grafting into networks

scientific article (publication date: 2001)

Introgression and genetic structure in northern Spanish Atlantic salmon (Salmo salar L.) populations according to mtDNA data

article

Inverted replication of vertebrate mitochondria

scientific article published on 21 February 2008

Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients

scientific article published on 31 January 2007

Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters

scientific article published on 04 February 2022

Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial

scientific article

Low-mitochondrial diversity and lack of structure in the velvet swimming crab Necora puber along the Galician coast

scientific article published in 2009

MODELTEST: testing the model of DNA substitution

scientific article

Mitochondrial DNA phylogeography and population history of the grey wolf canis lupus

scientific article (publication date: December 1999)

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests

scientific article

ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online

scientific article published on July 2006

Molecular phylogeny and biogeographic history of the European Maja spider crabs (Decapoda, Majidae)

scholarly article by Graciela Sotelo et al published October 2009 in Molecular Phylogenetics and Evolution

Molecular systematics of European Hyalodaphnia: the role of contemporary hybridization in ancient species

article

MtArt: A New Model of Amino Acid Replacement for Arthropoda

article

Multigene phylogeny of Malagasy day geckos of the genus Phelsuma

scientific article published on 9 April 2009

Multilocus inference of species trees and DNA barcoding

scientific article

Multiregional Tumor Trees Are Not Phylogenies

scientific article published on 17 July 2017

Mytilus galloprovincialis Lmk. in northern Africa

article

NGSphy: phylogenomic simulation of next-generation sequencing data

scientific article published on 9 March 2018

NGSphy: phylogenomic simulation of next-generation sequencing data

Nested clade analysis statistics

article

Nested clade phylogeographic analysis for conservation genetics

article

New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex

scientific article

On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy

scientific article (publication date: March 2006)

Origin and length distribution of unidirectional prokaryotic overlapping genes

scientific article published on 10 January 2014

PHYLOGEOGRAPHIC HISTORY OF THE LAND SNAIL CANDIDULA UNIFASCIATA (HELICELLINAE, STYLOMMATOPHORA): FRAGMENTATION, CORRIDOR MIGRATION, AND SECONDARY CONTACT

Parallel evolution of the genetic code in arthropod mitochondrial genomes.

scientific article

Perkinsoide chabelardi n. gen., a protozoan parasite with an intermediate evolutionary position: possible cause of the decrease of sardine fisheries?

scientific article published in June 2006

Pharmacogenetic study of statin therapy and cholesterol reduction

scientific article

Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand

scientific article

Phylodynamics of HIV-1 from a phase-III AIDS vaccine trial in North America

scientific article published on 28 October 2009

Phylogenetic Approaches to Molecular Epidemiology

scholarly article published 2002

Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): multiple natural colonisations, introductions and island radiations

scientific article published on 26 July 2006

Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail

scientific article published in July 2007

Phylogenetic models of molecular evolution: next-generation data, fit, and performance

scientific article

Phylogenetics of HIV

article

Phylogenomics for Systematic Biology

scientific article published in 2016

Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution

scientific article published on 25 April 2019

Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact

scientific article published in September 2002

Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands ⬇️

scientific article published on January 5, 2013

Phylogeography and speciation of colour morphs in the colonial ascidian Pseudodistoma crucigaster

scientific article published on 01 October 2004

Polymorphisms in the sequences of Marteilia internal transcribed spacer region of the ribosomal RNA genes (ITS-1) in Spain: genetic types are not related with bivalve hosts

scientific article published in June 2005

Population genetics of the porB gene of Neisseria gonorrhoeae: different dynamics in different homology groups

scientific article published in March 2000

ProtTest 3: fast selection of best-fit models of protein evolution

scientific article (publication date: 15 April 2011)

ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution

article published in 2011

ProtTest: selection of best-fit models of protein evolution

scientific article (publication date: May 2005)

Protein evolution along phylogenetic histories under structurally constrained substitution models.

scientific article

Proving universal common ancestry with similar sequences

scientific article published on May 2012

RDP2: recombination detection and analysis from sequence alignments

scientific article published on 17 September 2004

RDP3: a flexible and fast computer program for analyzing recombination

scientific article (publication date: October 2010)

RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues.

scientific article published on 24 September 2015

Rapid evolution and biogeographic spread in a colorectal cancer

scientific article published on 13 November 2019

Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography

scientific article

Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method

scientific article

Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy

scientific article

Recombination in evolutionary genomics

scientific article

SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission

scientific article published on 18 February 2021

Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1).

scientific article published in June 2001

Selecting the Best-Fit Model of Nucleotide Substitution

article

Selecting the best-fit model of nucleotide substitution

scientific article published in August 2001

Selection of models of DNA evolution with jModelTest

scientific article

Selective Pressures on Human Cancer Genes along the Evolution of Mammals

article

Sensitivity to sequencing depth in single-cell cancer genomics.

scientific article

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

scientific article

Simple (Wrong) Models for Complex Trees: A Case from Retroviridae

scientific article published in 2001

Simulating haplotype blocks in the human genome

scientific article published in January 2003

Simulation of coding sequence evolution

Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories

scientific article

Spatio-temporal genetic variability in sea trout (Salmo trutta) populations from north-western Spain

article

Spatio-temporal genetic variability of sea trout populations in Northwestern Spain

article

Species Tree Estimation from Genome-Wide Data with guenomu

scientific article

Species Tree Estimation from Genome-wide Data with Guenomu

TCS: a computer program to estimate gene genealogies

scientific article (publication date: October 2000)

Testing for universal common ancestry

scientific article published on 23 June 2014

The causes and consequences of HIV evolution

scientific article

The effect of branch length variation on the selection of models of molecular evolution

scientific article published in May 2001

The effect of recombination on the accuracy of phylogeny estimation

scientific article published in March 2002

The effect of recombination on the reconstruction of ancestral sequences

scientific article

The evolution and appearance of C3 duplications in fish originate an exclusive teleost c3 gene form with anti-inflammatory activity

scientific article

The evolution of the mitochondrial genetic code in arthropods revisited

scientific article

The evolutionary value of recombination is constrained by genome modularity

scientific article

The evolutionary value of recombination is constrained by genome modularity

scholarly article by Darren Patrick Martin published in January 2005

The inversion of the Control Region in three mitogenomes provides further evidence for an asymmetric model of vertebrate mtDNA replication

scientific article

The mussel Xenostrobus securis: a well-established alien invader in the Ria de Vigo (Spain, NE Atlantic)

article

Tree scanning: a method for using haplotype trees in phenotype/genotype association studies

scientific article

TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees

scientific article published on 28 January 2005

Unsorted homology within locus and species trees

scientific article published on 30 July 2014

Unveiling the Molecular Clock in the Presence of Recombination

scientific article published in 2001

Using MODELTEST and PAUP* to select a model of nucleotide substitution

scientific article published in February 2003

Using models of nucleotide evolution to build phylogenetic trees

scientific article

Widespread gene conversion of alpha-2-fucosyltransferase genes in mammals

scientific article published on 16 June 2009

Widespread recombination in published animal mtDNA sequences.

scientific article

jModelTest 2: more models, new heuristics and parallel computing

scientific article (publication date: 30 July 2012)

jModelTest: phylogenetic model averaging

scientific article (publication date: July 2008)

jmodeltest.org: selection of nucleotide substitution models on the cloud

scientific article

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