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Re: st: Sequence analysis: sqom full problem
From
[email protected] (Brendan Halpin)
To
[email protected]
Subject
Re: st: Sequence analysis: sqom full problem
Date
Tue, 01 Mar 2011 21:38:40 +0000
On Tue, Mar 01 2011, Office 2004 Test Drive User wrote:
> Perform 3665278 Comparisons with Needleman-Wunsch Algorithm
> Running mata function
SQOM uses Mata to calculate the pairwise distances, which is slow when
you're doing it 3.7 million times. Mata is normally fast for matrix operations
but not for explicit iteration such as is involved here.
I have written a plugin to do the same calculation, which is much faster
because it is written in C. However, it's not nicely packaged. The code
and instructions for installation are at
http://teaching.sociology.ul.ie/seqanal
Regards,
Brendan
--
Brendan Halpin, Department of Sociology, University of Limerick, Ireland
Tel: w +353-61-213147 f +353-61-202569 h +353-61-338562; Room F1-009 x 3147
mailto:[email protected] http://www.ul.ie/sociology/brendan.halpin.html
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