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torognes / vsearch

Versatile open-source tool for microbiome analysis
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Implement --cons_truncate clustering output option #25

Closed torognes closed 4 months ago

torognes commented 9 years ago

Need a fast multiple alignment algorithm

torognes commented 9 years ago

Options consout and msaout implemented in VSEARCH 0.2.0. Uses a center-star MSA algorithm with the centroid as the center. Haven't found out how cons_truncate works.

torognes commented 6 years ago

Uncertain what the cons_truncate option really do. Closing issue.

torognes commented 5 years ago

See https://www.drive5.com/usearch/manual7/opt_consout.html

torognes commented 5 years ago

Indicates that terminal gaps should be taken into account when computing consensus sequences. By default, usearch does not, meaning that these gaps are ignored and the consensus is built from the other symbols in the columns. VSEARCH currently never handles terminal gaps differently from other gaps when computing the consensus. A user have asked for an option to choose the behaviour (see issue #86). Perhaps this should be updated.

frederic-mahe commented 4 months ago

I suggest to close the issue for now. PotentialFuture tag allows us to find and revisit that issue if need be.