I have a question:
Is it possible to use align.seqs to align a .fasta file without comparing it to a reference database?
I have a huge database of fungal sequences without any kind of alignment and I would like to use it after as a reference for later alignments, as follows:
Thanks once again
Is it possible to have a .fasta file with the aligned sequences after running this command?
No, this will do all possible pairwise comparisons. To do an all vs. all multiple alignment, without a reference, you’d need to use something like MUSCLE or Clustal
The problem is that Muscle or Clustal servers do not allow to upload files as big as the ones I have.
Does anyone know how to solve this kind of problem?