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JTFouquier / ghost-tree

creating hybrid-gene phylogenetic trees for diversity analyses
BSD 3-Clause "New" or "Revised" License
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Improve code complexity in ghosttree.scaffold #33

Open JTFouquier opened 9 years ago

JTFouquier commented 9 years ago

Suggestion from D.M.: line 102, which determines which sequences to write out, is performing a list look up. This can be reduced to O(1). It is also not using the skbio fasta formatter.

JTFouquier commented 8 years ago

I'm re-labeling this issue because IMO it needs to be this way because of having to traverse through the genera and then find the corresponding accession number that matches the current genus. I thought about it a while, but I do think it's necessary to keep it as is.