align.seqs without reference

Hello again

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:

align.seqs(fasta=myfungalsequences.fasta, reference=myfungaldatabase.fasta)

Thanks once again

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You might try this:

Is it possible to have a .fasta file with the aligned sequences after running this command?

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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

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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?

Thanks again.