In article <paul-310394110903 at pandora.connect.com.au>,
Paul Davis <paul at connect.com.au> wrote:
>I'm posting this on behalf of a friend.
>She is working on the mammalian D-loop of mitochondrial DNA and is looking
>for a program that finds optimal sequence alignment and assigns gaps.
>It would be good if the software also does multiple alignments of both
>closely and distantly related species.
The "align" program in the FASTA package (available from
"virginia.EDU" in "pub/fasta/fasta17.shar.Z") will produce optimal
global alignment with gaps for DNA and protein sequences. It aligns
only two sequences at once. The only genuine optimal alignment
program for multiple sequences that I am aware of is "msa" (Lipman,
Altschul, and Kececioglu, (1989) PNAS 86:4412-4415) which is available