Tag Archives: phylogeny

What is ‘real-time’ phylogenomics?

Over the past few years I’ve been developing research, which I collectively refer to as ‘real-time phylogenomics’ – and this is the name of our mini-site for MinION-based rapid identification-by-sequencing. Since our paper on this will hopefully be published soon, … 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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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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