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Contents
Contents
User's Manual for FISH
(Fast Identification of Segmental Homology)
version 1.0
released 30 June 2003
Copyright 2003 University of North Carolina at Chapel Hill
Contents
Getting started
Introduction
Contact information
Legal information
Acknowledgements
Availability
Installing from source code
Installing the Windows executable
Installing the MacOSX executable
Testing FISH on sample data
How it works
Step 1: From markers to features
Step 2: From features to grid
Removing low ranking matches
Numbering of points
Enforcing symmetry
Defining the neighborhood size
Step 3: From grid to blocks
Choosing among multiple neighbors
Overlapping blocks
Parameters
Algorithmic parameters
Input and output parameters
File formats
Input files
Control file
Map files
Match files
Output
Screen output
Processing contigs
Processing matches
Processing blocks
Contig file
Grid file
Block file
Simple block file
An example
A control input file
A map input file
A match input file
An example of captured STDOUT
A contig output file
A grids output file
A blocks file
Bibliography
About this document ...
root 2003-06-27
