Tardigrade comparative genomics

There is now a second Tardigrade genome described in a manuscript (Koutsovoulos et al 2015), only days after the first (Boothby et al 2015– not OA). Koutsovoulos et al¬†however strongly suggests that the widely publicised rampant horizontal gene transfer (HGT) is problematic. This alternate genome¬†comes from Mark Blaxter’s group in Edinburgh, and has in fact…

ReproPhylo: a reproducible phylogenomics environment

Our new phylogenomics environment is called ReproPhylo. It makes experimental reproducibility frictionless, occurring quietly in the background while you work on the science. The environment has a lot of tools to allow exploration of phylogenomics data and to create phylogenomic analysis pipelines. It is distributed in a Docker container simplifying installation and allowing the reproducibility…

Genomics and ethics

There is a really interesting take on the ethics of human genomics from Dienekes’ Anthropology Blog prompted by the aboriginal genome recently released. I can’t say I disagree with anything. Potential bad ethical outcomes of genetic sampling are very rarely clearly explained and just left hanging in the air as something that must be true….

Calculating intron density

I have a project going at the moment to examine changes in intron diversity, size and location in animal genomes. I am always a bit frustrated with the way introns are treated in many genome characterisation papers- “the genome contained Y introns with mean intron size Xbp” is usually all we get. This sort of…