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Old 08-28-2014, 08:34 AM   #1
polarfire
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Location: Auburn, AL

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Default Script to count parsimony informative sites

I have hundreds of alignments, and I am curious if there is a script or tool out there that can simply count the number of parsimony informative sites in any given alignment?

I know you can get this information by loading it into a phylogenetics program (e.g. PAUP or MrBayes), but if anyone knows of a script that can do this so it can be automated and done quickly I'd appreciate it!
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Old 08-28-2014, 11:38 AM   #2
themerlin
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Default

No promises that it works correctly, but here's something that I had sitting around:

https://gist.github.com/jasonsahl/9306cd014b63cae12154

You need BioPython to run and it assumes no gaps. In addition to reporting the number of PI SNPs, it also prints a new multi-fasta with only those sites included. Feel free to edit it as you see fit.

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Old 08-28-2014, 12:24 PM   #3
polarfire
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Thanks for that script!

I also found out you can do it with the function pis() in the R library phyloch. That function also allows for gaps.
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