A deceptively simple question, but one that doesn't seem to have a simple answer. I tried doing it in several ways, but none of the tools I usually use gave the desired results.
The only way I have been able to get anywhere was a bit convoluted and requires access to the commercial program SeqMan (part of the Lasergene package from DNAStar). Import unaligned DNA sequence files into SeqMan and assemble them into a contig. You can adjust the consensus calling by playing about with the options in the SeqMan parameters. You can also edit the consensus by hand. Then all you need to do is save the consensus to a text file.
This is not precisely what you wanted, but it seems to be the best available.
Molecular Biology Unit Manager - Diagnostics & Molecular Biology Section
Science and Advice for Scottish Agriculture (SASA)
Does anyone know of software or a web page that will take a Clustal .aln
file and simply spew out a single consensus sequence?
I have an alignment of thirty 2000bp nucleotide sequences and ideally
want to simply stick a single letter consensus sequence into an
isothermal primer design program.
At the moment we are generating the consensus sequence by hand but it's
a pain to do!
I love deadlines. I especially like the whooshing noise they make as
they go flying by.