Request: don't rearrange sequence order

[SethMusker]

Hi Robert,

Is it possible to keep the order of the sequences in the output file the same as in the input? (I've been getting this with the latest windows and linux pre-compiled binaries, with -align, with each producing a different, seemingly random order).

Cheers,
Seth

p.s. I've been really happy with the quality of alignments from muscle5!

[rcedgar]

Thanks for the feedback. I'm aware of the "seemingly random" order issue. I was thinking the output should be sorted to bring similar sequences together (e.g. this can be done with a post-order traversal of the guide tree), but preserving the input order also makes sense as an option. On my list, but not sure when I will be able to work on it. In the mean time it's a few lines of python to re-arrange the sequences following the order of the input FASTA or a text file with a list of sequence identifiers.

[permia]

The esl-alimanip (in HMMER software) can solve the two situation easily. The option --tree in esl-alimanip may be used to bring similar sequences together. The option --reorder may be used to keep the order as the input fasta.