[Bioperl-l] error during installation

[Leon Timmermans]

On Tue, Jun 19, 2012 at 5:25 PM, Du, Peng <du at ibio.jp> wrote:
> As to the Clustalw problem, it turned out that, I didn't install it in
> the first place, I am very sorry for the stupid mistake. It is alright
> now. But, as to dpAlign, I compared the alignment of non coding
> regions of two species with dpAlign (in an Intel x86 but much slower
> machine where dpAlign is good) and Clustalw respectively and checked
> the output, I found that, each with default parameters, the alignments
> by dpAlign were better than that by Clustalw, and there was a
> tremendous difference in the outputs in terms of A<=>G, C<=>T, AG<=>CT
> substitutional rate and divergence by Tamura-Nei Model between the two
> alignments. The values are much smaller with dpAlign.  Since I am a
> newbie, I don't quite understand why there was such a difference. Is
> it might because of the Clustalw is designed for multiple alignment or
> the default parameters are not appropriate?
>
> I am now investigating other tools available in the main distribution
> of  BioPerl, but I have no idea whether there is a good substitution
> of dpAlign in context of non coding region alignment.

ClustalW uses a heuristic algorithm, it cannot produce a solution that
is guaranteed to be optimal. dpAlign uses the Miller-Myers algorithm
(a variant on Needleman-Wunch), that does make such guarantees. It
should be slower but may produce a better alignment.

Leon