A simple measure of distance is e.g. the number of amino acid differences of two sequences divided by the number of aligned amino acids. You can use the pairwise alignments to derive that number. There is also plenty of other ways to calculate evolutionary distances and many papers have been written on this topic...
Andreas On Tue, Apr 21, 2009 at 3:19 AM, JP <[email protected]> wrote: > Thanks Andreas - Would you say that evolutionary distance is the same as > pairwise alignment ? > > Many thanks > JP > > On Tue, Apr 21, 2009 at 12:26 AM, Andreas Prlic <[email protected]> wrote: >> >> Hi Jean-Paul, >> >> You can use BioJava to calculate pairwise alignments between your >> sequences: >> >> http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 >> >> Andreas >> >> >> On Mon, Apr 20, 2009 at 7:56 AM, JP <[email protected]> wrote: >> > Hi there at Biojava, >> > >> > I have a number of orthologue protein (sequences) from different species >> > - I >> > would like to calculate the distance (score) between each of these >> > (programatically) based on the sequence. >> > >> > Can anyone suggest a way to do this (I'd rather use an existing bit of >> > software than having to reinvent the wheel) ? Surely this software must >> > exist...(hopefully in biojava). >> > >> > Many Thanks >> > Jean-Paul Ebejer, Malta >> > _______________________________________________ >> > Biojava-l mailing list - [email protected] >> > http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
