[Biopython] alignment with clustalX

[George Devaniranjan]

Hi John,

I am no expert in clustalX alignments but you must remember that clustalX
will align "anything", basically I think your data is too divergent from
each other and clustal is creating "gaps" to "align" of course the end
alignment makes no sense now !
Hope it makes sense.

George


On Mon, Nov 4, 2013 at 5:09 PM, john fernando <fernando.j at inbox.com> wrote:

> Hi,
>
> I downloaded clustalX from the website and want to align the following
> fragments.
>
> I used a user defined substitution matrix.
>
> (Both the input and substitution matrix used are attached)
>
> I only selected fragments 23 +/- 1, so basically all the fragments are
> about the same length.
>
> I tried to follow the method outlined in "phylogenetic trees made easy" by
>  Barry Hall.
>
> Its not aligning well, lots of ----------lines appear.
>
> I tried to save the output to attach but didn't succeed saving as PS.
> (so sorry about that)
>
> Thank you,
> John
>
> ____________________________________________________________
> FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on
> your desktop!
> Check it out at http://www.inbox.com/marineaquarium
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>