Documentation, tutorials and cookbook about pairwise sequence alignment

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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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<div dir=3D"ltr"><div><div><div><div><div><div>Hello everyone.<br><br></div=
>I have been studying the pairwise sequence alignment concept for a project=
 that I need to do for an exam.<br></div><div>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.).<br></=
div>I would implement my project in Java employing indeed BioJava as starti=
ng point.<br></div><div>I set up correctly the Maven project on Eclipse so =
no problem under that point of view.<br></div><div><br></div>Few months ago=
 I have seen there was all the documentation, tutorials and specifications =
about the BioJava project based on the Wiki pages.<br></div>I have seen it =
has been all migrated into a new web site but now I am not finding any docu=
mentation, tutorial or cookbook about the topic of personal interest.<br><b=
r></div>- In the BioJavaTutorial page - book 2, the alignment module has no=
 pages of explanation.<br></div><div>- In the CookBook4.0, all the links re=
lative to the paiwise sequence alignment give me back an &quot;<span id=3D"=
result_box" class=3D"" lang=3D"en"><span>address</span> <span class=3D"">un=
interpretable</span></span>&quot; message.<br></div><div>- Finally in the W=
iki Pages section there are many links. In some of these there are links in=
teresting for me but they contain not well formatted codes.<br><br></div><d=
iv>I know that it may taketime to migrate all the things but in the meantim=
e:<br>Is there any possibility to have the reference to the old web site?<b=
r></div><div>Anyone can help me to indicate me where I can find some good p=
ages of documentation, tutorial, etc. about pairwise sequence alignment for=
 BioJava?<br><br></div><div>Thanks a lot.<br></div></div>

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