README for OrthoSelect
--------------------------

Test data
--------------------------------------------------------------------------------------------------------
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:
--------------------------------------------------------------------------------------------------------
	blastall
	hmmbuild
	hmmsearch
	genewise
	ESTScan
	muscle
	wget (optional)
	noisy (optional)
	t_coffee
	muscle

The following Environmental variables have to be set:
------------------------------------------------------------------------------
	WISECONFIGDIR
	ESTSCANDIR

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


The archive includes these files:
----------------------------------------------------
	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:
------------------------------------------------------------------------------
	User_guide.pdf