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Tag Archives: phylogenetics
BaTS (and Befi-BaTS), SHiAT, and Genome Convergence Pipeline have moved!
Important – please take note! Headline: All my phylogenetics software is now on GitHub, not websites or Google Code Please use the new FAQ pages and issue/bug tracker forms, rather than emailing me directly in the first instance Until now, … Continue reading
Posted in Coding, Science
Tagged BaTS, Befi-BaTS, coding, FAQ, genome convergence pipeline, github, googlecode, phylogenetics, software
1 Comment
Interpreting ‘tree space’ in the context of very large empirical datasets
Seminar presented at the Maths Department, University of Portsmouth, 19th November 2014 Evolutionary biologists represent actual or hypothesised evolutionary relations between living organisms using phylogenies, directed bifurcating graphs (trees) that describe evolutionary processes in terms of speciation or splitting events … Continue reading
Posted in Publications, Science, Talks
Tagged evolutionary biology, phylogenetics, topology, tree space
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HYPHY Hack: Passing arguments to HYPHY for phylogenetics using the command-line
[ Important update, 2017-Feb-07 ] [ This solution, already a bit hacky, should now be considered a last-resort. Sergei and colleague Stephen Weaver have suggested a much more elegant solution; see: https://github.com/veg/hyphy/issues/522. You’ll still have to dive into the batch file you want to … Continue reading
Reviewing FastCodeML, a potential replacement for PAML’s codeml
(first posted at SBCS-Evolve) Valle and colleagues have just released FastCodeML, an application for the detection of positive selection in DNA datasets. This is a successor SlimCodeML, which is itself an improved implementation of the codeml program from Ziheng Yang’s … Continue reading
Posted in Science
Tagged bioinformatics, codeml, dN/dS, fastCodeML, natural selection, PAML, phylogenetics, RAxML, review
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Using x-windows to render GUIs for server-client phylogenomics
The power of modern computers allied to high-throughput next-generation sequencing will usher in a new era of quantitative biology that will deliver the moon on a stick to every researcher on Earth… Well, quite. But something we’ve run up against … Continue reading
Our Nature paper! Genome-wide molecular convergence in echolocating mammals
Exciting news from the lab this week… we’ve published in one of the leading journals, Nature!!! Much of my work in the Rossiter BatLab for the last couple of years has centred around the search for genomic signatures of molecular … Continue reading
Posted in Journals, Publications, Science
Tagged convergent evolution, genome, phylogenetics, phylogenomics, publications
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Molecular epidemiology and phylogeny reveals complex spatial dynamics of endemic canine parvovirus.
J Virol. 2011 May 18. [Epub ahead of print] Clegg SR, Coyne KP, Parker J, Dawson S, Godsall SA, Pinchbeck G, Cripps PJ, Gaskell RM, Radford AD. Canine parvovirus 2 (CPV-2) is a severe enteric pathogen of dogs, causing high … Continue reading
Posted in Journals, Publications, Science
Tagged article, BaTS, canine parvovirus, CPV, j virol, journal, phylogenetics, phylogeography, spatial dynamics
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Generation of neutralizing antibodies and divergence of SIVmac239 in cynomolgus macaques following short-term early antiretroviral therapy.
PLoS Pathog. 2010 Sep 2;6(9):e1001084. Ozkaya Sahin G, Bowles EJ, Parker J, Uchtenhagen H, Sheik-Khalil E, Taylor S, Pybus OG, Mäkitalo B, Walther-Jallow L, Spångberg M, Thorstensson R, Achour A, Fenyö EM, Stewart-Jones GB, Spetz AL. Neutralizing antibodies (NAb) able … Continue reading
Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute Infection
Humphreys I, Fleming V, Fabris P, Parker J, Schulenberg B, Brown A, Demetriou C, Gaudieri S, Pfafferott K, Lucas M, Collier J, Huang KH, Pybus OG, Klenerman P, Barnes E. J Virol. 2009 Nov;83(22):11456-66. Epub 2009 Sep 9. Hepatitis C … Continue reading
Posted in Journals, Publications
Tagged bioinformatics, collaborations, HCV, hepatitis C virus, journals, phylogenetics, phylogeny, publications, science, virus
2 Comments
The within- and among-host evolution of chronically-infecting human RNA viruses
A research thesis submitted for the degree of Doctor of Philosophy at the University of Oxford. J Parker Funded by: Natural Environment Research Council (UK) with support from Linacre College, Oxford. Abstract: This thesis examines the evolutionary biology of the … Continue reading
Posted in Publications, Theses
Tagged AIDS, BaTS, Befi-BaTS, bioinformatics, HCV, HIV, phylogenetics, publications, Thesis, virology, Viruses
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