Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.
The sort.seqs command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order. You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.