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linnabrown / run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
http://bcb.unl.edu/dbCAN2
GNU General Public License v3.0
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Question: why hmmscan and not hmmsearch #105

Closed SilasK closed 8 months ago

SilasK commented 2 years ago

Would it make sense to use hmmsearch instead of hmmscan?

http://cryptogenomicon.org/hmmscan-vs-hmmsearch-speed-the-numerology.html

linnabrown commented 2 years ago

Thank you so much for the suggestion. Since hmmsearch does not share the same data format as hmmscan, we do not use hmmsearch. We will consider how to replace hmmscan with hmmsearch in an appropriate way in the future.

linnabrown commented 8 months ago

Thank you!, We replaced hmmscan with hmmsearch in our new version now (4.1.1), which supports multiple CPUs. Thank you for bringing this out.