[Bioperl-l] Fwd: Announcing Ngila 1.2.1 Alignment Program

Hilmar Lapp hlapp at duke.edu
Tue Aug 28 18:13:32 EDT 2007


Is anyone thinking about adding support for this as an aligner  
option? I'm not sure whether aside from a Bio::Tools::Run module we'd  
also need a format parser - it sounds like it's emitting clustalw  
format?

	-hilmar

Begin forwarded message:

> From: evoldir at evol.biology.mcmaster.ca
> Date: August 28, 2007 3:02:19 AM EDT
> To: hlapp at duke.edu
> Subject: Other:  Announcing Ngila 1.2.1 Alignment Program
> Reply-To: racartwr at ncsu.edu
>
>
> Ngila is a global, pairwise alignment program that uses logarithmic  
> and
> affine gap costs, i.e. C(g) = a+b*g+c*ln(g).  These gap costs are more
> biologically realistic than the more popular (and efficient) affine  
> gap
> cost model.
>
> I have recently completed updating the program to version 1.2.1.  The
> new version includes two new, evolutionary alignment models based  
> on my
> current research.  These models allow you to find the maximum  
> alignment
> of two sequences based on biological, evolutionary parameters---no  
> more
> guessing at biological costs.  Additional changes are noted on the  
> website.
>
> Website & Manual:
>
> http://scit.us/projects/ngila/
>
> Windows Binary:
>
> http://scit.us/projects/files/ngila/Releases/ngila-release-win32.zip
>
> Unix/Mac Source Code:
>
> http://scit.us/projects/files/ngila/Releases/ngila-release.tar.gz
>
> I'll be happy to answer any questions users have about the new  
> models or
> the program.
>
> -- 
> *********************************************************
> Reed A. Cartwright, PhD     http://scit.us/
> Postdoctoral Researcher     http://www.dererumnatura.us/
> Department of Genetics      http://www.pandasthumb.org/
>
> Bioinformatics Research Center
> North Carolina State University
> Campus Box 7566
> Raleigh, NC 27695-7566
>

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
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