[Biojava-l] BioJava Question - Evolutionary Rate Calculation

[Andreas Prlic]

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 <jp at javaclass.co.uk> 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 <andreas at sdsc.edu> 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 <jp at javaclass.co.uk> 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
>> > _______________________________________________
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>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>
>