Multiple Alignment software for huge amount of peptide sequences/cysteine framework

[LucasVS]

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[colindaven]

I wouldn't align with Excel .... scripts are very slow in it, and I doubt you'll find a bioinformatician willing to touch it!

Why not try muscle, thats a nice quick bit of software. Perhaps muscle can also align cysteines only, with the gap characters (-) you put in. Otherwise maybe subsitute all other amino acids with a fairly neutral amino acid (perhaps Alanine). You can then see if the alignment is mainly determined by the cysteines.

[me_myself_andI]

Hello,

Excel for storing sequence data and/or VBA for scripting is a very bad idea in this context.

Try the following:
Convert your sequences to Fasta format (plain text) and use either Muscle (muscle -maxiters 1 -in your-fasta-file) or Mafft (mafft -auto your-fasta-file)

Andreas

[*#1*]

I also suggest Muscle http://www.drive5.com/muscle/