Hi I would like to do alignment of multiple peptide sequences. I want output as ungapped alignments. Which tools are there apart from Clustal to do this job? Thank you in advance.
Normally gaps are inserted as part of the alignment algorithm for clustalw, if you are looking for "ungapped alignment" the only way I can think of is setting a high -gapopen penalty.
I'm not sure if there is a tool that will suit specifically to your situation, but you can find useful links to various MSA tools in one of my older answers: A: Analysis of a conserved motif across a phylum
hm, there is an issue with the URL, the correct link is A: Analysis of a conserved motif across a phylum
sorry about that, we have a bug there, it seems the autolink will override the reference citation just paste the link as whole like this and it will transform it Analysis Of A Conserved Motif Across A Phylum
I am usually quite happy with the results from the T-Coffee multiple sequence alignment server: http://tcoffee.crg.cat/
Did not use it for this particular purpose though, but with the right parameter setting (e.g. using local aligners for the pairwise alignment step, running T-coffee in 'Advanced' mode setting the '-gapopen' and '-gapext' parameters to very high values, e.g. 1000) you should be able to do what you want.
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if you do need to insert gaps, wouldn't your input fasta file be the same as your output? I guess I do not get the point of the exercise...
I should have said this before, I do not want gaps inside the sequences but gaps can be present only at the end of the alignments. Just to say this is not an homework, I want to know if there is any tool which can do the ungapped alignment within the sequence and gaps can be given only in the ends of sequence? I hope I am not making it complicated.
I would try what Hranjeev suggested. Use a really high gap open penalty. Do not use clustalW (el al) these aligners want to align the beginning and end.