README

README for OrthoSelect
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Test data
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The directory "project1" contains a test run using publicly available ESTs.


The following executable have to be in your path so that OrthoSelect can correctly work:
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	blastall
	hmmbuild
	hmmsearch
	genewise
	ESTScan
	muscle
	wget (optional)
	noisy (optional)
	t_coffee
	muscle

The following Environmental variables have to be set:
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	WISECONFIGDIR
	ESTSCANDIR

The following ESTScan matrices will be used (put them in the ESTSCANDIR)
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	At.smat
	Dm.smat
	Dr.smat
	Hs.smat
	Mm.smat
	Rn.smat


The archive includes these files:
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	README
	INSTALL
        perl_scripts/auto_download.pl
	perl_scripts/create_taxa_file.pl
	perl_scripts/gene_selection.pl
	db/
	lib/
	lib/Blaststuff.pm
	lib/Iostuff.pm
	options.txt
	perl_scripts/
	perl_scripts/post_processing.pl
	perl_scripts/prepare_analysis.pl
	perl_scripts/select_best_ortholog.pl
	perl_scripts/start_blasto_nucleotide.pl
	perl_scripts/start_filter_redundant_cluster.pl
	perl_scripts/start_filter_redundant_single.pl
	perl_scripts/start_orthology_assignment_cluster.pl
	perl_scripts/start_orthology_assignment_single.pl
	perl_scripts/stats.pl
	est_libraries/
	User_guide.pdf
	

The documentation is available as a pdf document:
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	User_guide.pdf