Author Archives: Joe

HYPHY hack: Passing arguments to HYPHY via the command line

(NB: Reposted from Joe’s blog) HYHPY, is a great platform for advanced phylogenetics by Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse, where abstract concepts such as likelihood-ratio tests, model selection, and phylogenetic inference are represented … Continue reading

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Installing Ubuntu 12.04 LTS on a Dell Windows 8 machine with UEFI

Quick post this – both in case anyone’s interested and in case something breaks and we have to remember what we did, exactly (the far more likely scenario) Ubuntu. Everyone loves it – probably the world’s easiest dual-boot install going … Continue reading

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First Look: FastCodeML vs. codeml (PAML)

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 workhorse phylogenetic analysis package … Continue reading

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Heading South for the winter

The rainy cold weather which traditionally marks winter in London is finally here, a little later than traditional but misery-making nonetheless (non-UK residents note: unlike your puny winters, in the British Isles winter rocks from about September to May, with … Continue reading

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Playing around with x-windows for server-client analyses

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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