Torbjørn Rognes
Yes, `regex.h` has been removed as it not used anymore. Have also updated name of binary on Windows to `swarm.exe` in commit f480695992a0a28a4f902b179dc154833a8c473f.
Considering the relatively low number of computers in use with AVX2 and the rather limited time now spend on computing alignments, this performance improvement with AVX2 is currently rather limited.
Or use https://github.com/RonnySoak/libssa
Parasail looks interesting and flexible. A master student of mine have been working on another solution which I think is generally faster: https://github.com/RonnySoak/libssa His master thesis will soon be available....
Sounds like a good idea!
Exactly which variant of the BSD license will be used for QIIME 2?
@outpaddling, if there are small changes I can do to vsearch to increase compatibility with older usearch versions and help you adapt it for use with qiime, please tell me.
The --query, --evalue and --targetalnfract options are also not recognized by vsearch. Do you know which version of usearch this is supposed to be? usearch 5.2.236 or usearch 6.1 or...
Added in commit 4880186cf5d39ff3bc468098b583b91008c9a0ab.
Feature added in version 2.19.0 just released.