drwxr-xr-x	root/root	usr/
drwxr-xr-x	root/root	usr/bin/
-rwxr-xr-x	root/root	usr/bin/guidance
drwxr-xr-x	root/root	usr/lib/
drwxrwxr-x	root/root	usr/lib/guidance/
drwxrwxr-x	root/root	usr/lib/guidance/libs/
drwxrwxr-x	root/root	usr/lib/guidance/libs/phylogeny/
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/.project
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/HIVb.dat.q
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/HIVw.dat.q
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/LG.dat.q
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/adrianCodon.dat.q
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/cmdline.ggo
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/cpREV45.dat.q
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/dayhoff.dat.q
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/evolObjs.args
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/evolObjs.header
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/jones.dat.q
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/mtREV24.dat.q
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/phylogeny.ncb
drwxrwxr-x	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/HIVBetween.dat
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/HIVWithin.dat
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/cpREV45.dat
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/dayhoff.dat
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/jones.dat
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/mitochondriaAscidian.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/mitochondriaEchinoderm.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/mitochondriaFlatworm.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/mitochondriaInvertebrate.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/mitochondriaProtozoan.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/mitochondriaVertebrate.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/mitochondriaYeast.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/mtREV24.dat
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/nuclearBlepharisma.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/nuclearCiliate.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/nuclearEuplotid.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/nuclearStandard.code
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/replacementMatrixSource/wag.dat
-rw-rw-r--	root/root	usr/lib/guidance/libs/phylogeny/wag.dat.q
drwxrwxr-x	root/root	usr/lib/guidance/programs/
drwxrwxr-x	root/root	usr/lib/guidance/programs/isEqualTree/
-rwxr-xr-x	root/root	usr/lib/guidance/programs/isEqualTree/isEqualTree
drwxrwxr-x	root/root	usr/lib/guidance/programs/msa_set_score/
-rwxr-xr-x	root/root	usr/lib/guidance/programs/msa_set_score/msa_set_score
drwxrwxr-x	root/root	usr/lib/guidance/programs/removeTaxa/
-rwxr-xr-x	root/root	usr/lib/guidance/programs/removeTaxa/removeTaxa
drwxrwxr-x	root/root	usr/lib/guidance/programs/semphy/
drwxrwxr-x	root/root	usr/lib/guidance/programs/semphy/progs/
-rw-rw-r--	root/root	usr/lib/guidance/programs/semphy/progs/bootstrap_prog.ggo
-rwxr-xr-x	root/root	usr/lib/guidance/programs/semphy/semphy
-rw-rw-r--	root/root	usr/lib/guidance/programs/semphy/semphy.args
-rw-rw-r--	root/root	usr/lib/guidance/programs/semphy/semphy.ggo
drwxrwxr-x	root/root	usr/lib/guidance/www/
drwxrwxr-x	root/root	usr/lib/guidance/www/Guidance/
-rw-rw-r--	root/root	usr/lib/guidance/www/Guidance/GUIDANCE_CONSTANTS.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/Guidance/Guidance.pm
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/Remove_Pos_bellow_Cutoff.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/Remove_Seq_bellow_Cutoff.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/code2nameFasta.pl
drwxrwxr-x	root/root	usr/lib/guidance/www/Guidance/exec/
drwxrwxr-x	root/root	usr/lib/guidance/www/Guidance/exec/HoT/
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/HoT/COS.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/HoT_COS_GUIDANCE2.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/code2nameTree.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/convertBSTrees2MafftFormat.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/name2codeFastaFrom1.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/newick2mafft.rb
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/printColoredAlignment.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/pullOutBStrees.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/removeLowSPsites.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/rootTree.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/exec/runAlignBStrees.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/failedCheck.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/guidance.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Guidance/maskLowScoreResidues.pl
drwxrwxr-x	root/root	usr/lib/guidance/www/Selecton/
-rwxr-xr-x	root/root	usr/lib/guidance/www/Selecton/calculate_statistics.pl
-rw-rw-r--	root/root	usr/lib/guidance/www/Selecton/codonAlign.pm
-rwxr-xr-x	root/root	usr/lib/guidance/www/Selecton/colorCoding.v2.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/Selecton/colorCodingLinear.pl
-rw-rw-r--	root/root	usr/lib/guidance/www/Selecton/kill_process.cgi
-rw-rw-r--	root/root	usr/lib/guidance/www/Selecton/pipe_for_selecton.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/Selecton/selecton_qsub.cgi
-rwxr-xr-x	root/root	usr/lib/guidance/www/Selecton/selecton_run_calc.pl
-rw-rw-r--	root/root	usr/lib/guidance/www/Selecton/statTest.cgi
-rwxr-xr-x	root/root	usr/lib/guidance/www/Selecton/statTest.pl
drwxrwxr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/BIOSEQUENCE_FUNCTIONS.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/BlastResultsForm.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/ConSeq_gradesPE_and_Outputs.pm
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/Create_Chimera_Figure_Files_For_ConSurfDB.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/Create_PyMol_Files_For_ConSurfDB.pl
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/GENERAL_CONSTANTS.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/GENERAL_CONST_LECS.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/HandleQueue.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/MSA_parser.pm
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/Monitor_Bioseq_Node.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/Replace_B_Factor_With_ConSurf_Grade.pl
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/SELECTON_CONSTANTS.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/TREE_parser.pm
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/blastpgp_to_fasta.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/checkjob.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/cluster.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/convertNacessFormat.pl
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/cp_rasmol_gradesPE_and_pipe.pm
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/create_MSA_from_blast.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/create_chimerx.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/create_colored_chimera_msa.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/daemon.pl
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/design_pipe.pm
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/extract_info_from_pdb.pl
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/new_PDB_insertion.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/new_rate4site_routines.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/old_parseFiles.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/parseFiles.pm
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/r4s_res_to_gradesPE.pl
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/rasmol_gradesPE_and_pipe.pm
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/rate4site_routines.pm
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/remove_old_results.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/sendEmail.pl
-rw-rw-r--	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/sequence_visualization.pm
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/test_time.pl
-rwxr-xr-x	root/root	usr/lib/guidance/www/bioSequence_scripts_and_constants/update_runTime.pl