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I downloaded some datasets from the SILVA96 database. These are structurally aligned SSU rDNA sequences. I browsed through the taxonomic groups and chose annelids (N=1050) and nematodes (N=5048) as smallish tests. I downloaded these as fasta files.I started with the...

The prediction I made before about a long silence once this year's students turned up was sadly accurate. Anyway, students dealt with, grant proposal submitted, lectures (mostly) given, bureaucracy reduced (a bit), time to get on with some phylogenetics.I...

In order to to see how quickly FastTree runs for me I need some automated method of timing it. While some programs like phyML return a runtime at the end FastTree doesn't seem to. So I searched the web and...

This is how I downloaded, compiled and got FastTree working. Its a bit obvious in places but I think detailed instructions are a good thing to have out there and Google findable. I am using a multicore MacPro 2.8GHz with...

So when I started writing this blog I thought I would use it to outline some of the things I was working on as I went along. Not real projects, which I will write up and publish, but side projects...

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