[Bioperl-l] conservative amino acid change?

[Heikki Lehvaslaiho]

Aaron,

Looks like we are doing Jason's ScriptCentral thingy here. 8-)

Your plan of starting slowly with simpler tasks and then adding more
complex approaches sounds good. 

Could you send me all modules you think are relevant in one or several
files so that I can get the feel of them and put together a plan how
to start putting the code into bioperl.


	-Heikki

Aaron J Mackey wrote:
> 
> On Mon, 6 Aug 2001, Heikki Lehvaslaiho wrote:
> 
> > > > Bio::Matrix::SimilarityMatrix
> > > > Bio::Matrix::SimilarityMatrixIO
> > > > Bio::Matrix::SimilarityMatrixIO::full
> > > > Bio::Matrix::SimilarityMatrixIO::half
> 
> FYI, I also have some perl code to deal with the various
> 
> (strict)? (upper|lower) triangular matrices
> 
> that these things tend to be stored as.  It's currently my home-baked
> version of Math::Matrix::Bool::Triangular (i.e. it uses
> Math::Matrix::Bool, which itself is only using Bit::Vector).
> 
> Let me know if you need these array index i <-> matrix indices i,j
> conversion equations.
> 
> -Aaron
> 
> --
>  o ~   ~   ~   ~   ~   ~  o
> / Aaron J Mackey           \
> \  Dr. Pearson Laboratory  /
>  \ University of Virginia  \
>  /  (434) 924-2821          \
>  \  amackey@virginia.edu    /
>   o ~   ~   ~   ~   ~   ~  o

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