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JLSteenwyk / ClipKIT

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
https://jlsteenwyk.com/ClipKIT/
MIT License
63 stars 4 forks source link

Code used to benchmark #41

Closed sen-pai closed 10 months ago

sen-pai commented 10 months ago

Thanks for this really useful library! I'm trying to find the code you have used to compare ClipKIT with other methods (the graphs shown here).

if you have written any wrappers around trimAI, Gblocks (whose source code I cant seem to find) and BMGE, could you please share them too?

JLSteenwyk commented 10 months ago

Hi @sen-pai,

Thank you for writing and for using ClipKIT!

With respect to the desirability-based framework for ranking, I used the general framework detailed, including R code, here: integRATE from Eidem et al. (2018) BMC Medical Genomics.

For trimAl, I used: trimal -in <inputfile> -out <outputfile> -gappyout; trimal -in <inputfile> -out <outputfile> -strict; and trimal -in <inputfile> -out <outputfile> -strictplus.

For GBlocks, I used default parameters. I, too, am having trouble finding the source code since the original domain seems to be stalling. However, I found this link to a web portal version http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=gblocks.

I hope this helps!