Dear Firer,

You can use MUSCLE.

Kindly go through  the link below

http://www.ebi.ac.uk/Tools/msa/muscle/

Hope for the best.

 this website may provide you with the neccessary tool: http://www.expasy.org/resources

Thanks Koner for the link. I got the tree results, but am not sure how to interpret the significance of the numeric data

Thanks Michael. I have that link, but from all the possibilities there, I'm still not sure which would be the best to try

did you try the website bioz.com?  That site may be useful.

Thanks veery much Michael

Dear Firer,

you could try the ugene program to align the sequences with any of the alignment options and generate a consensus sequence

another option to identify conserved motifs is the MEME suite

http://meme-suite.org/tools/meme

hope you find this helpful

kind regards

Samuel

tHANK YOU sAMUEL. i'LL LOOK THROUGH THEM

Hi Michael,  

We recently developed a tool, ASC+MEME, that could find motifs from massive peptide sequences. Check the following link for more information. Any feedbacks are welcomed. Thanks.

http://www.cs.ucsb.edu/~honglei/abp/index.htm

Best,

Honglei