[Biojava-l] Documentation, tutorials and cookbook about pairwise sequence alignment

[Andrea Battistelli]

Hello everyone.

I have been studying the pairwise sequence alignment concept for a project
that I need to do for an exam.
In particular I am interested in the global and local alignments and all
the things related to them (how they are implemented, how I can generate a
paiwise alignment, ect.).
I would implement my project in Java employing indeed BioJava as starting
point.
I set up correctly the Maven project on Eclipse so no problem under that
point of view.

Few months ago I have seen there was all the documentation, tutorials and
specifications about the BioJava project based on the Wiki pages.
I have seen it has been all migrated into a new web site but now I am not
finding any documentation, tutorial or cookbook about the topic of personal
interest.

- In the BioJavaTutorial page - book 2, the alignment module has no pages
of explanation.
- In the CookBook4.0, all the links relative to the paiwise sequence
alignment give me back an "address uninterpretable" message.
- Finally in the Wiki Pages section there are many links. In some of these
there are links interesting for me but they contain not well formatted
codes.

I know that it may taketime to migrate all the things but in the meantime:
Is there any possibility to have the reference to the old web site?
Anyone can help me to indicate me where I can find some good pages of
documentation, tutorial, etc. about pairwise sequence alignment for BioJava?

Thanks a lot.
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