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(parent: 6b89b31) | patch
initial commit
authorcmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Wed, 9 Feb 2011 01:20:06 +0000 (01:20 +0000)
committercmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Wed, 9 Feb 2011 01:20:06 +0000 (01:20 +0000)
commit253a714c2440558d7c70fe30cac5d7b093798968
tree465a06ada2b87183f2cee8187002f7019343b28etree | snapshot
parent6b89b31381f9fb3df64152a90a18a39b47cf5e49commit | diff
initial commit
72 files changed:
forester/ruby/00_README.txt [new file with mode: 0644] blob
forester/ruby/evoruby/exe/d2f.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/dsx.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/evo_nursery.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/fae.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/fasta_tap.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/hsp.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/msa_pro.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/mse.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/phylogenies_decorator.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/phylogeny_factory.rb [new file with mode: 0644] blob
forester/ruby/evoruby/exe/run_phylo_pipeline.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/tap.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/test.rb [new file with mode: 0755] blob
forester/ruby/evoruby/exe/tseq_tap.rb [new file with mode: 0755] blob
forester/ruby/evoruby/files/00_phylogeny_factory.template [new file with mode: 0644] blob
forester/ruby/evoruby/files/00_sample_tap_mapfile [new file with mode: 0644] blob
forester/ruby/evoruby/files/test/fasta_file.txt [new file with mode: 0644] blob
forester/ruby/evoruby/files/test/general_msa_file.txt [new file with mode: 0644] blob
forester/ruby/evoruby/files/test/ncbi_tseq.xml [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/domain_sequence_extractor.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/domains_to_forester.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/evo_nursery.rb [new file with mode: 0755] blob
forester/ruby/evoruby/lib/evo/apps/fasta_extractor.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/fasta_taxonomy_processor.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/hmmscan_parser.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/msa_processor.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/new_tap.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/phylogenies_decorator.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/phylogeny_factory.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/taxonomy_processor.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/apps/tseq_taxonomy_processor.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/msa_io.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/parser/basic_table_parser.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/parser/fasta_parser.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/parser/general_msa_parser.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/parser/hmmsearch_domain_extractor.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/parser/msa_parser.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/parser/ncbi_tseq_parser.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/parser/sp_taxonomy_parser.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/writer/fasta_writer.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/writer/msa_writer.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/writer/nexus_writer.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/io/writer/phylip_sequential_writer.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/msa/msa.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/msa/msa_factory.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/sequence/domain_structure.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/sequence/protein_domain.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/sequence/sequence.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/soft/fastme.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/soft/raxml.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/soft/resource_locations.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/soft/tree_puzzle.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/table/basic_table.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/taxonomy/sp_taxonomy.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/taxonomy/taxonomy.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/util/command_line_arguments.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/util/constants.rb [new file with mode: 0644] blob
forester/ruby/evoruby/lib/evo/util/util.rb [new file with mode: 0644] blob
forester/ruby/scripts/delete_ext_nodes.rb [new file with mode: 0755] blob
forester/ruby/scripts/hmm_split.rb [new file with mode: 0755] blob
forester/ruby/scripts/parameters.rb_dir_qsub [new file with mode: 0644] blob
forester/ruby/scripts/pfam2go_reformat.rb [new file with mode: 0755] blob
forester/ruby/scripts/pfam_summarize.rb [new file with mode: 0755] blob
forester/ruby/scripts/pfam_to_scop.rb [new file with mode: 0755] blob
forester/ruby/scripts/rb_dir_qsub.rb [new file with mode: 0644] blob
forester/ruby/scripts/rb_dir_x.rb [new file with mode: 0644] blob
forester/ruby/scripts/rb_qsub.rb [new file with mode: 0755] blob
forester/ruby/scripts/replace.rb [new file with mode: 0755] blob
forester/ruby/scripts/replace_id.rb [new file with mode: 0644] blob
forester/ruby/scripts/scoptastic.rb [new file with mode: 0755] blob