Actual Science…

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 and how I got them to work (or otherwise). Unfortunately there hasn’t been much of that, lots of reviews and comment instead. Hopefully I am going to change that now. 

Last April I posted about FastTree, the rapid NJ application that seems to be able to handle approx 40,000 OTUs. The authors say 

“FastTree inferred a phylogeny for an alignment of 39,092 proteins, including support values, in half an hour on a desktop PC”.

I actually compiled and started using it back in April, but got swamped by teaching and theses and stuff and never posted anything more. My next few posts are going to be about getting FastTree to work and how it copes with some of my datasets. Alternatively as the new crop of undergraduates arrive next week there may be a long silence instead.

2 Comments Add yours

  1. Karen Cranston says:

    How timely… I’d be very interested in hearing about your experiences with FastTree. We just discussed it in a lab meeting and it’s on my list of possible programs for a large-scale tree building project.


  2. Dave Lunt says:

    Hi Karen, looks good so far. I’m going to continue posting my tests. I only ran the previous version once or twice but it looks promising. I’m probably going to use a test database at first of about 1000 sequences of SSU rDNA (about 1700bp) then move up to many more taxa (I hope). It may take me a few weeks to go through this. If you have your own experiences first feel free to fill up the comments section.Dave


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