I enjoyed this cartoon from xkcd (via genetic future).
Tag: Perl
FastTree 2: Timing runs
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 found bits of perl code to put a script timer together. I have uploaded the…
Perl scripts for phylogenetics
The script I referred to in my last post is actually seqConverter.pl written by Olaf Bininda-Emonds, with a few minor modifications to send the output directly to phyml. I thought I would flag up his site which has a large and very useful collection of perl scripts for phylogenetic data wrangling. These are open-source scripts…
Droppable applications from scripts
I’m not a very competent perl programmer. Even writing the word programmer here makes me slightly embarrassed. I do carry out frequent sequence conversions and manipulations with perl scripts I’ve put together though. Sometimes when I need to run a script many times I’ve found the most irritating thing is launching the scripts and pointing…
Annotating trees with Treedyn
In order to really get information out of building phylogenetic trees (especially large ones) some thought has to be given to how to annotate the tips (OTUs).The two programs that seem to do this in a powerful way are ARB and Treedyn. I also want to explore Tree-Q vista, which looks promising, but haven’t really…
EvoPhylo 