de Oliveira Martins L, Posada D. Infinitely long branches and an informal test of common ancestry. Biology Direct (11), 19 (2016) doi:10.1186/s13062-016-0120-y

  Mallo D, de Oliveira Martins L, Posada D. SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees. Systematic Biology 65(2), 334 – 344 (2016) doi:10.1093/sysbio/syv082

  de Oliveira Martins L, Mallo D, Posada D. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Systematic Biology 65(3), 397 – 416 (2016) doi: 10.1093/sysbio/syu082

  Mallo D, de Oliveira Martins L, Posada D. Estimation of Species Trees. eLS. a0025781 (2014) doi:10.1002/9780470015902.a0025781

  Mallo D, de Oliveira Martins L, Posada D. Unsorted Homology within Locus and Species Trees. Systematic Biology 63(6), 988 – 992 (2014) doi: 10.1093/sysbio/syu050

  de Oliveira Martins L and Posada D. Testing for Universal Common Ancestry. Systematic Biology 63(5), 838 – 842 (2014) doi: 10.1093/sysbio/syu041

  de Oliveira Martins L, Mallo D, Posada D. Phylogenetic Likelihood. eLS. a0005141 (2013) doi:10.1002/9780470015902.a0005141

  Bizinoto MC, Yabe S, Leal E, Kishino H, de Oliveira Martins L, Lima ML, Morais ER, Diaz RS and Janini LM. Codon pairs of the HIV-1 vif gene correlate with CD4+ T cell count. BMC Infectious Diseases 13, 173 (2013) doi:10.1186/1471-2334-13-173

  de Oliveira Martins L and Posada D. Proving universal common ancestry with similar sequences. Trends in Evolutionary Biology 4(1), e5 (2012) doi:10.4081/eb.2012.e5

  Miyazaki J, de Oliveira Martins L, Fujita Y, Matsumoto H and Fujiwara Y. Evolutionary Process of Deep-Sea Bathymodiolus Mussels. PLoS ONE 5(4), e10363 (2010) doi:10.1371/journal.pone.0010363

  de Oliveira Martins L, Kishino H. Distribution of distances between topologies and its effect on detection of phylogenetic recombination. Annals of the Institute of Statistical Mathematics 62 (1), 145 - 159 (2010) doi:10.1007/s10463-009-0259-8

  Sawai H, Otani H, Arisue N, Palacpac N, de Oliveira Martins L, Pathirana S, Handunnetti S, Kawai S, Kishino H, Horii T, Tanabe K. Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of Plasmodium vivax and related simian malaria parasites. BMC Evol Biol 10(1), 52 (2010) doi:10.1186/1471-2148-10-52

  de Oliveira Martins L, Leal É and Kishino H. Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees. PLoS ONE 3(7), e2651 (2008) doi:10.1371/journal.pone.0002651

  Leal É, de Oliveira Martins L, Janini LM, Diaz RS. Evolutionary Dynamics of HIV-1 BF and CB Recombinants and Its Parental Counterparts in South America. Retrovirology: Research and Treatment 1, 1 (2008)

  Watabe T, Kishino H, de Oliveira Martins L, Kitazoe Y. A Likelihood-based Index of Protein Protein Binding Affinities with Application to Influenza HA Escape from Antibodies. Molecular Biology and Evolution 24 (8), 1627 – 1638 (2007) doi:10.1093/molbev/msm079

  Iwasaki H, Kyuno A, Shintaku M, Fujita Y, Fujiwara Y, Fujikura K, Hashimoto J, de Oliveira Martins L, Gebruk A, Miyazaki J. Evolutionary relationships of deep-sea mussels inferred by mitochondrial DNA sequences. Marine Biology 149 (5), 1111 - 1122 (2006) doi:10.1007/s00227-006-0268-6

  Mihara M, Sakai T, Nakao K, de Oliveira Martins L, Hosoya K, Miyazaki J. Phylogeography of Loaches of the Genus Lefua (Balitoridae, Cypriniformes) Inferred from Mitochondrial DNA Sequences. Zoological Sciences 22(2), 157 – 168 (2005) doi:10.2108/zsj.22.157


   de Oliveira Martins L and Posada D. Species Tree Estimation from Genome-wide Data with Guenomu. Bioinformatics Volume I: Data, Sequence Analysis, and Evolution. (Methods in Molecular Biology Series). 2nd Edition. Edited by Jonathan M. Keith. Humana Press, Springer, 461 – 478 (2017). ISBN: 978-1-4939-6620-2  [biorxiv'ed under doi: 10.1101/023861]

  Costa M and de Oliveira Martins L. Acceptance of Evolution. Um livro sobre EvoluçãoA book about Evolution»). Edited by Rita Campos. Centro de Investigação em Biodiversidade e Recursos Genéticos de Portugal, 22 – 26 (2013). ISBN: 978-989-97418-9-8 [download PDF]

  de Oliveira Martins L. Viral genomic recombination: HIV subtyping and detecting new variants HIV 実践生物統計学—分子から生態まで Biostatistics in Practice: from the Molecule to Ecology»). Edited by the Biometrics Laboratory at the University of Tokyo. Asakura Shoten, 148 – 164 (2004). ISBN/ISSN: 978-4254420272 [find at]


  Schliep K, Paradis E, de Oliveira Martins L, Potts A, White TW, Stachniss C, and Kendall M. Package ‘phangorn’. The comprehensive R archive network (2017). Available at

  de Oliveira Martins L. Bayesian Inference of Viral Recombination: Topology distance between DNA segments and its Distribution. Ph.D. thesis presented at the University of Tokyo, Japan (2008) doi:10.6084/m9.figshare.5144857

  de Oliveira Martins L. Simulation of the Molecular Evolution of HIV-1 Analysis of genetic diversity estimates. Masters Thesis presented at the University of Sao Paulo, Brazil (2002) doi:10.6084/m9.figshare.5144686

  de Oliveira Martins L. fprotml: Protein analysis using maximum likelihood. Currents in Computational Molecular Biology (RECOMB 2001). ACM Press, 197 – 198 (2001)

  de Oliveira Martins L, Zanotto PMA. Amino Acid Substitution Matrices Estimated by Maximum Likelihood. Genome Informatics (12), 380 – 381 (2001) doi:10.11234/gi1990.12.380