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

Chris Fields cjfields at uiuc.edu
Wed Aug 29 00:01:13 EDT 2007


It probably wouldn't be hard to write one up, particularly if it's  
got already parsable format.  We could probably base it off the  
current clustalw wrapper unless someone else thinks there is a better  
way.

chris

On Aug 28, 2007, at 5:13 PM, Hilmar Lapp wrote:

> 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
>> 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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