https://github.com/fabsta/orthoselect

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
https://github.com/fabsta/orthoselect

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OrthoSelect: a protocol for selecting orthologous groups in phylogenomics

• Host: GitHub
• URL: https://github.com/fabsta/orthoselect
• Owner: fabsta
• Created: 2011-10-17T20:51:32.000Z (about 13 years ago)
• Default Branch: master
• Last Pushed: 2011-10-17T20:51:44.000Z (about 13 years ago)
• Last Synced: 2023-10-20T19:47:18.512Z (about 1 year ago)
• Language: Perl
• Size: 691 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README

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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