Tag Archives: bioinformatics

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

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18th Evolutionary Biology Meeting – Storify!

[View the story “18th Evolutionary Biology Meeting in Marseille” on Storify] Tweet this Digg Post to LinkedIn Slashdot Stumble This

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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

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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

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Befi-BaTS v0.1.1 alpha release

Long-overdue update for beta version of Befi-BaTS. Software: Befi-BaTS Author: Joe Parker Version: 0.1.1 beta (download here) Release notes: Befi-BaTS v0.1 beta drops support for hard polytomies (tree nodes with > 2 daughters), now throwing a HardPolytomyException to the error … Continue reading

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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

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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

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Journal Impact Factors – a good free tool

(originally posted on Kitserve.org.uk) Recently, I’ve taken on more consulting work outside my own immediate area. http://www.eigenfactor.org, a free impact factor tool, has been incredibly handy. Here’s why. Getting to grips (well on some level, at least) with a new … Continue reading

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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

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Estimating the Date of Origin of An HIV-1 Circulating Recombinant Form

Virology. 2009 Apr 25;387(1):229-34. Epub 2009 Mar 9. Tee KK, Pybus OG, Parker J, Ng KP, Kamarulzaman A, Takebe Y. HIV is capable of frequent genetic exchange through recombination. Despite the pandemic spread of HIV-1 recombinants, their times of origin … Continue reading

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