MSA2

 

Uses principal component analysis to improve a set of footprints


Usage
msa2 <input 1> <input 2> <output 1> <output 2> <number of components>[CONVERGE=30]
 
<input 1> Input file to be processed as in  msa
<input 2> 2nd input file to be reprojected using the vectors determined for the first input
<output 1> reduced version of <input 1>
<output 2> reduced version of <input 2>
<# components> number of footprint variables too keep in the output file
[CONVERGE=30] number of number of convergence iterations to use. Default is 30. 

Typical Usage
msa2 proj.fp start.fp proj.msa.fp start.msa.fp 6

Description
This program works just like msa, but in addition to reducing the dimensionality of one footprint file, it also takes the basis vectors generated for the first input file and uses them to reproject a second input file. The latter file is therefore improved.  This is used to simultaneously reduce the dimensionality of 2 footprint files which later need to be compared, eg - for use with classesrefs.
 
 
 

EMAN Copyright 1997-8 Steve Ludtke, Phil Baldwin