Torbjørn Rognes
A user requested an option to exclude terminal gaps with `maxdiffs` when searching. The terminal gaps are currently included in the count used with `maxdiffs`. So an option to ignore...
A user suggested an option to sort OTU tables by decreasing abundance.
In order to support pipelines (e.g. qiime) that depend on older versions of usearch it would be an advantage if vsearch could be compatible and support options in older versions...
The multiple sequence alignment algorithm used in VSEARCH, the centre-star method, is rather simple. Consider implementing a better algorithm. As a start, unaligned residues to the left of the first...
The left or right part of the alignment shown in uchimealn files may contain long parts of the A and B parent sequences that are not aligned to the query....
Adapt SWARM to [AVX2](https://en.wikipedia.org/wiki/Advanced_Vector_Extensions#Advanced_Vector_Extensions_2) and the 256-bit registers available in the new Intel Haswell CPUs that became available in June 2013. Should allow 32-way SIMD parallellisation.
It has been suggested to allow the randseed option to be used with the sintax command since the algorithm has a random element and can give different results.
A few commands only allow FASTA files as input, and not FASTQ files, even though it would be simple and useful for them to also accept FASTQ files. This applies...
There should be an option to output the reason why merging failed with each pair of reads when using the `fastq_mergepairs` command. I think usearch has an option for this....