Author Archives: Joe

Camberwell Green consultation closing – reject these plans!

(Reposted from SouthwarkCyclists.org.uk…) Southwark Council propose expensive and disruptive alterations to Camberwell Green junction and area. The plans are terrible. Southwark Cyclists have thoroughly examined their proposal with expert advice and we have decided to formally reject these plans.    Please respond to the … Continue reading

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Omics in extreme Environments (Lightweight bioinformatics)

Presentation on lightweight bioinformatics (Raspi / cloud computing) for real-time field-based analyses. Presented at iEOS2015, St. Andrews, 3-6th July 2015. Slides [SlideShare]: cc-by-nc-nd Tweet this Digg Post to LinkedIn Slashdot Stumble This

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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

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Embedding Artist profiles, playlists, and content from Spotify in HTML

Quick post this – turns out Spotify have added a really cool new function to their desktop application: You can now right-click any resource in Spotify (could be an artist, a playlist, a profile or a track or album) and get a … Continue reading

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Parsing numbers from multiple formats in Java

We were having a chat over coffee today and a question arose about merging data from multiple databases. At first sight this seems pretty easy, especially if you’re working with relational databases that have unique IDs (like, uh, a Latin … Continue reading

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Application note: ‘Befi-BaTS’ version 0.10.1 – Error rate and statistical power of distance-based measures of phylogeny-trait association.

In prep. SUMMARY Building on work presented previously (Parker et al., 2008), we study a number of more complex measures of phylogeny-trait association (implemented in the program Befi-BaTS / BaTS v0.10.1) which take into account the branch lengths of a … Continue reading

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Molecular convergence and adaptive evolution in constant-frequency echolocating Chiroptera detected in phylogenomic datasets

In prep. Manuscripts in progress (all rights reserved – you may not copy or distribute these files; content and conclusions subject to change; strictly embargoed until publication in a peer-reviewed journal/book): v1: .doc   Tweet this Digg Post to LinkedIn Slashdot … Continue reading

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Application note: CONTEXT, a Phylogenomic Dataset Browser

In prep. (v3 – 14 Jun 2017) Summary. The CONTEXT (COmparative Nucleotides and Trees Exploration Tool) is a phylogenomics dataset browser that consists of a Java API and an executable binary jarfile with graphical user interface (GUI) for the high-throughput analysis … Continue reading

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Detection of molecular convergence – literature review

In prep. (v2 – 21 April 2015) Abstract Convergent evolution is a process by which neutral evolutionary processes and adaptive natural selection in response to niche specialisation lead to similar forms arising in unrelated taxa. Phenotypic convergence has been appreciated … Continue reading

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In support of… taxis

Here’s where I’m coming from with this one. Let me say it simply: More regular cyclists means lower private car ownership, less congestion for taxis to deal with, and more non-car-owners taking taxi trips. OK, now for the detailed bit… … Continue reading

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