[Biojava-l] can BioJava do alignment ?

[Ramon Medrado]

Hi,

The information is true. Biojava 1.5  has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz

and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar

and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz

I wait to have helped

-- 
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil



2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that      BioJava 1.5 can do alignment itself (e.g., I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
>    is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
>    itself ?

   if it does, I downloaded the CVS view of BioJava 1.5, but could not find

>    any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
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