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FastTree (Read 4161 times)
Mar 20th, 2015 at 4:36am

Stephan   Offline
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Please consider the incorporation of FastTree (found at microbesonline.org/fasttree) into UGENE.
The multi processor version compiles nicely under Cygwin.

For one of our projects, with more than 100000 SNPs, we had to compile with the USE_DOUBLE option and had to decrease MLMinBranchLength and MLMinRelBranchLength by two log10 steps to get a nice resolution of the smaller branches of the tree. I suggest to always use these modified setting as processing time is not increased unreasonable.

 
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Reply #1 - Mar 20th, 2015 at 8:11pm

German Grekhov   Offline
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Novosibirsk

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Hello, Stephan. Thank you so much for your request! We have created the issue about it in our bug-tracker: https://local.ugene.unipro.ru/tracker/browse/UGENE-4178
Maybe, it will be implemented in one of future UGENE versions.

I don't not understand how phylogenetic trees refer to SNPs. Could you explain it, please?
 
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