I am trying to use Mercator to perform a HOMOVA analysis and for doing this the sequences in the distance matrix need to be in order so that all sequences from the same treatment are clustered together in the matrix. Is there any way to get the aligned sequences in the same order as the input file?
You can sort the alignment file according to grouping. Also, the sequences should be in the same order that you inputted them. Remember that you can’t use a name file with mercator so you can’t do a unique.seqs on them. Thanks for reminding me that the code is out there. I guess we should get that into mothur at some point.