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rcedgar / usearch12

Open-source usearch
https://drive5.com/usearch
GNU General Public License v3.0
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no ublast? #5

Closed jianshu93 closed 1 week ago

jianshu93 commented 2 weeks ago

Hello Robert,

usearch -ublast is not open source right, but I do saw usearch_local there, just some default parameter tuning for usearch_local and then we have ublast?

Thanks,

Jianshu

rcedgar commented 2 weeks ago

The story is a bit complicated because ublast (the command in usearch) and UBLAST (the algorithm described in my 2010 paper) are not the same. This is confusing, my mistake. The UBLAST algorithm is implemented in the usearch_local command.

The ublast command implemented a different algorithm which used seed indexing. This is now obsolete because DIAMOND is better, I see no reason anyone would use ublast now unless there are some older scripts which require it.

If you want to use ublast for backwards compatibility with a pipeline, you can use one of the older usearch binaries which are now posted under the CC0-1.0 license: https://github.com/rcedgar/usearch_old_binaries/.

jianshu93 commented 2 weeks ago

Hi Robert,

Thanks for the response. Diamond is only for amino acid index, not nt but ublast does support nt right. Yeah I can use the old binary for ublast but again I want to use it also for macOS M series CPU. Not sure it will be widely used since Mac is still less used in real world dataset. Thanks for open source (especially the local one) for the community.

Jianshu