Hey Marjan,

two hints:

1.) you should clarify your questions. Sometimes it is hard to understand. Why do you want to edit manually a multiple alignment? Which distance matrix did you use for the generation of the multiple alignment?

2.) I would ask this question again in the bioinformatics and computational biology group

Good luck

Ijad

Hi you need to clearly ask the question. Are you interested in DNA or protein multiple alignment? If It is regular sequence alignments you can try either GeneDoc or Bio edit. If you are doing protein homology modeling then parameters and way to address the multiple alignment will change where you need to consider the secondary structure of the protein and other things also.