[Biopython] alignment with clustalX

[john fernando]

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

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