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README.md

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+Msatfinder-2.0.9, taken from:
+
+http://web.archive.org/web/20071026090642/http://www.genomics.ceh.ac.uk/msatfinder/

README.txt

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+Msatfinder README, Last Updated July 2006
+Authors: Milo Thurston ([email protected]) and Dawn Field
+([email protected])
+The latest version of this software is available at:
+
+http://www.bioinf.ceh.ac.uk/msatfinder/downloads/msatfinder-latest.tar.gz
+or
+http://www.bioinf.ceh.ac.uk/msatfinder/downloads/msatfinder-latest.zip
+
+This file describes the installation and usage of the msatfinder program
+for the detection of microsatellite repeats. For full instructions,
+please see the msatfinder user manual. Please send comments, suggestions,
+or bug reports to the authors.
+
+
+INSTALLATION
+
+1.	Download the latest version of the msatfinder tar/zip file and unpack
+it.
+
+[~user] tar zxvf msatfinder-latest.tar.gz *
+[~user] cd msatfinder-<version>
+
+*or unzip msatfinder-latest.zip
+
+2.	If you require that the program be available to all users, then 
+copy the script to your preferred location, e.g.
+
+[msatfinder-<version>] sudo cp msatfinder /usr/local/bin
+
+3. Make sure the following dependencies are installed and configured on
+your system, or on your PATH in the case of EMBOSS &c.:
+
+Perl modules:
+- Bioperl
+- CGI
+- Config::Simple
+- File::Copy
+- File::Basename
+- Getopt::Std
+- Term::ReadLine
+- List::Util
+
+Software:
+EMBOSS (eprimer3)
+Primer3_core
+
+BASIC CONFIGURATION AND USAGE
+
+To check that your package and all dependencies are installed and
+configured correctly, test data is supplied (two baculovirus genomes in
+Genbank format).
+
+1. Read through the default values in msatfinder.rc, and change anything that
+you think might require altering (e.g. types and thresholds of msats to be
+searched for). This is probably not necessary for most searches.
+
+2.	To run the search, type:
+
+./msatfinder *gbk
+or
+./msatfinder *sprot
+
+An example Swissprot and Genbank file is provided.
+
+Output from this search will be found in the directories Fasta/,
+Repeats/, Msat_tabs/, Flank_tabs/, and Primers/. An html index
+containing hyperlinks to all the output files will be created as
+Repeats/results.html. Open in your preferred web browser to view
+the results.
+
+For further details on how to set up searches of your own data, please see the 
+Msatfinder user manual.
+
+If you experience any problems running this software, please write to
+the authors.