Publications
(2021) BAli-Phy version 3: model-based co-estimation of alignment and phylogeny. Bioinformatics 37(18) [doi: 10.1093/bioinformatics/btab129]
.(2020) Brazeau NF, Mitchell CL, Morgan AP, Deutsch-Feldman M, Watson OJ, Thwai KL, Waltmann A, Emch M, Gartner V, The epidemiology of Plasmodium vivax among adults in the Democratic Republic of the Congo. Nat Commun 12:4169. [doi: 10.1038/s41467-021-24216-3]
, Wray G, Mwandagalirwa MK, Tshefu AK, Likwela JL, Edwards JK, Verity R, Parr JB, Meshnick SR, Juliano JJ.(2017) McTavish EJ, Drew BT, How and Why to Build a Unified Tree of Life. BioEssays 39(11) [doi: 10.1002/bies.201700114]
, Cranston KA.(2017) A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species. PeerJ [doi: 10.7717/peerj.3058]
, Holder MT.(2015) A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation. Genetics 201:1171-1188 [doi: 10.1534/genetics.115.179093]
, Kumagai SK, Wang L, Tatarenkov A, Sakai AK, Weller SG, Culley TM, Avise JC, Uyenoyama MK.(2014) Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection. Mol. Biol. Evol. 31(8):1979-1993 [doi: 10.1093/molbev/msu174]
.(2012) Sliwa L, Miadlikowska J, Are widespread morphospecies from the Lecanora dispersa group (lichen-forming Ascomycota) monophyletic? The Bryologist, 115:265-277. [10.1639/0007-2745-115.2.265]
, Molnar K, and Lutzoni F.(2012) Law SHW, Comparative Genomics of Duplicate γ-Glutamyl Transferase Genes in Teleosts: Medaka (Oryzias latipes), Stickleback (Gasterosteus aculeatus), Green Spotted Pufferfish (Tetraodon nigroviridis), Fugu (Takifugu rubripes), and Zebrafish (Danio rerio). JEZ part B, 318B(1):35-49, [doi: 10.1002/jez.b.21439]
, Kullman SW.(2012) Revell LJ, Mahler DL, Peres-Neto PR, and A new method for identifying exceptional phenotypic diversification. Evolution, 66(1):135-146 [doi: 10.1111/j.1558-5646.2011.01435.x]
.(2011) Gaya E, Align, or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study. Mycologia, 103(2):361-378. [doi: 10.3852/10-120]
, Pere Navarro-Rosinés, Xavier Llimona, Miquel de Cáceres, Lutzoni F.(2009) Liang LJ, Weiss RE, Improving phylogenetic analyses by incorporating additional information from genetic sequence databases. Bioinformatics, 25(19):2530-2536. [WWW]
, Suchard MA.(2009) Lamm K, Reconstructing ancestral ranges in historical biogeography: properties and prospects. Journal of Systematics and Evolution,47(5):369-382 [WWW]
.(2008) Choi SC, Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences. Philosophical Transactions of the Royal Society B, 363(1512):3931-3939. [WWW]
, Thorne JL.(2007) Incorporating Indel Information into Phylogeny Estimation for Rapidly Emerging Pathogens. BMC Evolutionary Biology, 7:40 [WWW]
, Suchard MA.(2006) Suchard MA, BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics, 22(16):2047-2048 [WWW]
.(2005) Joint Bayesian Estimation of Alignment and Phylogeny. Systematic Biology, 54(3):401-418 [WWW] [Winner of Mitchell Prize in 2006]
, Suchard MA.Book chapters
(2019) Taxonomic Supertree Construction with Incertae sedis Taxa. Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, 29. Springer, Cham. pp. 151-173.
, Holder, MT.(2009) Robust inferences from Ambiguous Alignments. Sequence Alignment. University of California Press. pp. 209-270. [PDF]
, Suchard, MA.Work in progress...
- Bayesian phylogenies unplugged: majority consensus trees with wandering taxa. [PDF]