Mugen-UMAP: UMAP visualization and clustering of mutated genes in single-cell DNA sequencing data von Li, Teng, Zou, Yiran, Li, Xianghan, Wong, Thomas K F, Rodrigo, Allen G

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Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data von Drummond, Alexei J, Nicholls, Geoff K, Rodrigo, Allen G, Solomon, Wiremu

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An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes von Wong, Thomas K F, Li, Teng, Ranjard, Louis, Wu, Steven H, Sukumaran, Jeet, Rodrigo, Allen G

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Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage von Ranjard, Louis, Wong, Thomas K F, Rodrigo, Allen G

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Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage von Ranjard, Louis, Wong, Thomas K F, Rodrigo, Allen G

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Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing... von Ranjard, Louis, Wong, Thomas K F, Rodrigo, Allen G

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Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution von Nascimento, Fabrícia F, Rodrigo, Allen G

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HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations von Wong, Thomas K F, Ranjard, Louis, Lin, Yu, Rodrigo, Allen G

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HIV-1 transmission during early antiretroviral therapy: evaluation of two HIV-1 transmission events in the HPTN 052 prevention study von Ping, Li-Hua, Jabara, Cassandra B, Rodrigo, Allen G, Hudelson, Sarah E, Piwowar-Manning, Estelle, Wang, Lei, Eshleman, Susan H, Cohen, Myron S, Swanstrom, Ronald

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Modeling the Site-Specific Variation of Selection Patterns along Lineages von Guindon, Stéphane, Rodrigo, Allen G., Dyer, Kelly A., Huelsenbeck, John P., Felsenstein, Joseph

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MAST: Phylogenetic Inference with Mixtures Across Sites and Trees von Wong, Thomas K F, Cherryh, Caitlin, Rodrigo, Allen G, Hahn, Matthew W, Minh, Bui Quang, Lanfear, Robert

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Time‐dependent rates of molecular evolution von HO, SIMON Y. W., LANFEAR, ROBERT, BROMHAM, LINDELL, PHILLIPS, MATTHEW J., SOUBRIER, JULIEN, RODRIGO, ALLEN G., COOPER, ALAN

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Immune-Mediated Positive Selection Drives Human Immunodeficiency Virus Type 1 Molecular Variation and Predicts Disease Duration von Ross, Howard A, Rodrigo, Allen G

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Covariation of branch lengths in phylogenies of functionally related genes von Li, Wai Lok Sibon, Rodrigo, Allen G

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Complete mitochondrial genome of the green-lipped mussel, Perna canaliculus (Mollusca: Mytiloidea), from long nanopore sequencing reads von Ranjard, Louis, Wong, Thomas K. F., Külheim, Carsten, Rodrigo, Allen G., Ragg, Norman L. C., Patel, Selina, Dunphy, Brendon J.

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Associations between HLA Class I Alleles and Escape Mutations in the Hepatitis B Virus Core Gene in New Zealand-Resident Tongans von ABBOTT, William G. H, TSAI, Peter, LEUNG, Euphemia, TREVARTON, Alex, OFANOA, Malakai, HORNELL, John, GANE, Edward J, MUNN, Stephen R, RODRIGO, Allen G

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Phylogenetic Analysis of Feline Immunodeficiency Virus in Feral and Companion Domestic Cats of New Zealand von HAYWARD, Jessica J, TAYLOR, John, RODRIGO, Allen G

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SQUINT: a multiple alignment program and editor von Goode, Matthew G., Rodrigo, Allen G.

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Transient Compartmentalization of Simian Immunodeficiency Virus Variants in the Breast Milk of African Green Monkeys von Ho, Carrie, Wu, Steven, Amos, Joshua D, Colvin, Lisa, Smith, Shannon D, Wilks, Andrew B, Demarco, C Todd, Brinkley, Christie, Denny, Thomas N, Schmitz, Joern E, Rodrigo, Allen G, Permar, Sallie R

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pgHMA: Application of the heteroduplex mobility assay analysis in phylogenetics and population genetics von Li, Teng, Wong, Thomas K. F., Ranjard, Louis, Rodrigo, Allen G.

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