There is a piece of software called CD-HIT that can be useful in filtering out identical or very similar sequences from a set. Filtering out only 100% identical sequences is, of course, trivial. You can do it with "sort" and "uniq" plus some string manipulation glue on any linux command line. However, you could find CD-HIT useful if for some reason you wanted to change 100% to say 98% or 95%. Subsequently, you could multiply-align the sequences as suggested by Danish. If you wanted the repeated sequences to weigh more in the final alignment for some reason, you could also do the filtering step after aligning the sequences, I suppose.

Clustal Omega could be an option, or t-coffee too

There is a piece of software called CD-HIT that can be useful in filtering out identical or very similar sequences from a set. Filtering out only 100% identical sequences is, of course, trivial. You can do it with "sort" and "uniq" plus some string manipulation glue on any linux command line. However, you could find CD-HIT useful if for some reason you wanted to change 100% to say 98% or 95%. Subsequently, you could multiply-align the sequences as suggested by Danish. If you wanted the repeated sequences to weigh more in the final alignment for some reason, you could also do the filtering step after aligning the sequences, I suppose.

absolutely agree with previous opinion

You can test tophat or bowtie

I think the popular alignment viewer JalView has a built-in option to remove redundancy (not sure if before or after alignment, or both may be possible). Just open your multi-FASTA file, e.g., then call an aligner (e.g. MAFFT) as a webservice from the menu. Before or after that (as I said, just chech the options), set the appropriate similarity cutoff...

http://www.jalview.org

http://www.jalview.org/help/html/calculations/redundancy.html

Note the program also builds trees (or calls tree building tools) based on the resulting alignment, if you want.

HTH,

Rob

Agree with all the suggestion, but if you required you can go for EMBOSS package, there are different tool available for alignment.