[Savannah-hackers] submission of NeoBio - savannah.nongnu.org

[sergioanibaljr]

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Sergio Anibal de Carvalho Junior <address@hidden> described the package as 
follows:
License: gpl
Other License: 
Package: NeoBio
System name: neobio
Type: non-GNU

Description:
NeoBio is a Java class library of computational biology algorithms. The initial 
version will consist mainly of pairwise sequence alignment algorithms such as 
the classical dynamic programming methods of Needleman & Wunsch (global 
alignment) and Smith & Waterman (local alignment). A more efficient approach, 
due to M. Crochemore, G. Landau and M. Ziv-Ukelson (2002) will also be 
available.



All sequence alignment algorithms will support simple scoring schemes as well 
as substitution matrices such as standard BLOSUM and PAM matrices with constant 
(linear) gap penalty functions only. Future versions may contain related 
algorithms such as multiple sequence alignment, database search and protein 
structure prediction.



NeoBio will also provide simple GUI and command line based tools to run the 
sequence alignment algorithms on DNA and protein sequences.



No source code is available online at the moment.



Other Software Required:
No dependencies; NeoBio will use core Java packages only, these will propably 
include IO and Collections.

Other Comments:



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