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matsengrp / gctree

GCtree: phylogenetic inference of genotype-collapsed trees
https://matsengrp.github.io/gctree
GNU General Public License v3.0
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Any parallel or accelerated parameters? #66

Closed liyi522 closed 2 years ago

liyi522 commented 2 years ago

I think this tool is more suitable for B cell germline tree construction than other traditional tools.

But I have some trouble when I infered the tree for a large number of sequences (~300 unique sequences). As your advise, I have add the parameters like "dnaml" and "quick". But it was not working, it have taken more than 6 hours and it is still working. Any other parameters for multithreaded or speeding up of gctree? I would appreciate it if I could get an answer.

Looking forward your reply.

wsdewitt commented 2 years ago

It sounds like the slow part of this process is the parsimony tree generation, which relies on the phylip package. It does take a long time with this many sequences, and there isn't much we can do about it in the immediate term, unfortunately.