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ACH.pm  1.7  9 years  disz  changed doc to say XXserver->new() insetad of XX->new
ACHserver.pm  1.16  9 years  parrello  Removed from the SAS distribution.
ALITRE.pm  1.6  7 years  fangfang  add server side implementation of alignments_metadata_by_md5() and alignment...
ALITREserver.pm  1.1  8 years  parrello  New alignment/tree server stuff.
ANNO.pm  1.13  7 years  olson  Finish support for detailed kmers in dna.
ANNOserver.pm  1.26  7 years  olson  Add support for passing -detailed through to dna kmers. Add support for retrievi...
AT.pm  1.6  8 years  fangfang  add blast function
ATserver.pm  1.2  9 years  fangfang  default url set to biobig
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
AliTreeIdConvert.pm  1.1  8 years  golsen  Functions for interconverting MD5 and peg ids of alignments and trees in the SEE...
AliTreeSims.pm  1.8  8 years  fangfang  fixed a variable name
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
AliasAnalysis.pm  1.13  7 years  parrello  Added IMG and ERIC.
AlignTree.pm  1.51  5 years  fangfang  add CoreSEED db
AlignsAndTrees.pm  1.17  7 years  fangfang  add server side implementation of alignments_metadata_by_md5() and alignment...
AlignsAndTreesServer.pm  1.25  5 years  golsen  Copy documentation to top of module.
AnnoClearinghouse.pm  1.44  10 years  wilke  Modified sql query to ? syntax
Annotation.pm  1.4  11 years  parrello  Added a TITLE statement for the Wiki.
ApplyTransactions.pm  1.7  11 years  parrello  Changed POD format for better compatability with Wiki.
Assignments.pm  1.17  11 years  overbeek  remove impact of our annotations on making assignments using auto_assign
BBasicLocation.pm  1.1  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
BadCall.pm  1.4  11 years  parrello  Replaced obsolete AddToListMap method.
BasicLocation.pm  1.24  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
BerkTable.pm  1.2  9 years  olson  fix arg
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
Biochemistry.pm  1.2  5 years  overbeek  update reaction stuff
BlankSVP.pm  1.1  8 years  olson  Script & infrastructure for creating easy seedviewer pages.
Blast.pm  1.5  11 years  overbeek  close TMP files in Blast.pm
BlastInterface.pm  1.13  5 years  golsen  Copy the percIdentity option value to minIden when using blastall -p blastn.
Boolean.pm  1.3  6 years  overbeek  handle debug str better
ButtonArray.pm  1.1  11 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
CGIAlignTreeViewer.pm  1.24  6 years  golsen  Convert image files to use new temporary file name functions.
CO.pm  1.6  9 years  disz  changed doc to say XXserver->new() insetad of XX->new
COPYING.TXT  1.1  13 years  olson  add license file
COserver.pm  1.13  9 years  parrello  Removed from the SAS distribution.
CallByProjection.pm  1.4  7 years  overbeek  ross fixes
ChromosomalClusters.pm  1.11  8 years  parrello  Added "roles_to_proteins" method.
Classes.pm  1.1  13 years  mkubal  added Organism class
Clearinghouse.pm  1.7  5 years  olson  Don't spit output to stdout.
Clearinghouse.py  1.12  7 years  olson  Use new SS clearinghouse on pubseed.
ClientThing.pm  1.31  7 years  golsen  Test for an undefined value of $response->header('client-warning')
CloseGenomes.pm  1.2  7 years  olson  add sas tag
CloseStrains.pm  1.17  5 years  olson  Re-merge RAST chagnes.
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
Cluster.pm  1.11  13 years  olson  Added license words.
ClusterWorker.pm  1.2  13 years  olson  Added license words.
Clustering.pm  1.6  9 years  overbeek  added double and triple linkage
Cmd2HTML.pm  1.11  6 years  overbeek  add compound_to_reactions
CodonUsageTable.pm  1.4  6 years  golsen  Support for getting codon usage and genes from different genomes.
CommonCGI.pm  1.1  6 years  olson  common cgi code.
CompareMR.pm  1.8  10 years  paczian  cutting comments off of functional roles
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
Construct.pm  1.2  13 years  olson  Added license words.
ContigMD5.pm  1.3  12 years  olson  clone the digest so that checksum() may be called multiple times
Contigs.pm  1.1  10 years  overbeek  new Contigs.pm and compare_coding.pm
CorrTableEntry.pm  1.5  8 years  overbeek  add 20th column - clear_bbhs
Correspondence.pm  1.4  8 years  overbeek  correct the identity check
CorrespondenceCache.pm  1.2  8 years  parrello  Added experiment filter to "fid_experiments". Fixed correspondence cache to work...
Corresponds.pm  1.1  7 years  overbeek  finally debugged
CrossSeedLinks.pm  1.1  5 years  golsen  Rudimentary support for links between SEEDs. Nothing currenly uses it, but it se...
DBKernel.pm  1.82  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
DBrtns.pm  1.27  13 years  overbeek  Fix extra-args option to go at teh start of the list.
Diagram.pm  1.22  6 years  seaver  Removing STDERR debug statements from Diagram.pm
Dlits.pm  1.6  6 years  olson  Catch bad pmids so db call doesn't crash.
DocUtils.pm  1.18  10 years  parrello  Added documentation functions to the Sapling server.
DrugResistanceDB.pm  1.1  6 years  overbeek  drug resistance reps db
ErrorMessage.pm  1.2  9 years  olson  remove unused use CGI.
ExpressionDir.pm  1.12  8 years  olson  add compute_pearson_corr
FBAMODELserver.pm  1.5  8 years  chenry  Moving FBAMODELserver.pm to FigKernelPackages, and changing URL.
FBasicLocation.pm  1.1  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
FC.pm  1.22  6 years  parrello  Fixed to improve performance of pairset deletions.
FF.pm  1.36  6 years  olson  Add SAS declarations.
FFB3.pm  1.1  7 years  olson  figfam build helper module
FFs.pm  1.58  5 years  olson  Tie the translation btree.
FFserver.pm  1.23  9 years  parrello  Removed from the SAS distribution.
FIG.pm  1.918  5 years  olson  Genome object read/write to seed dir changes.
FIG.py  1.13  13 years  olson  Added license words.
FIG2.py  1.2  13 years  olson  Added license words.
FIGAttributes.pm  1.4  10 years  overbeek  get rid of something
FIGGenDB.pm  1.6  13 years  olson  Added license words.
FIGM.pm  1.22  5 years  olson  Rollup of RASTtk changes.
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
FIGRules.pm  1.56  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
FIGStatisticalModels.pm  1.8  6 years  gdpusch  mean() modified to use round-off-protected Kahan summation. stdev() modified to ...
FIGUtilities.pm  1.2  13 years  olson  Added license words.
FIGV.pm  1.103  5 years  olson  Rollup of RASTtk changes.
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
FIGgjo.pm  1.5  8 years  golsen  Support for better role coloring and formatting.
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
FIGnet.pm  1.2  13 years  olson  Added license words.
FIGrpc.pm  1.3  13 years  olson  Added license words.
FIGtree.pm  1.3  13 years  olson  Added license words.
FS_RAST.pm  1.39  7 years  overbeek  fix default of genetic code
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FileLocking.pm  1.4  9 years  olson  Changes for DesktopRast. CVHnS: ------------------------------------------------...
Find_RNAs.pm  1.5  5 years  olson  cleanup work directories
FudgeTransactions.pm  1.4  11 years  parrello  Changed POD format for better compatability with Wiki.
FullLocation.pm  1.25  9 years  parrello  Added a method to compute the total location length.
GenerateClusters.pm  1.2  6 years  overbeek  require % iden >= 50 for projection: UNTESTED
GenoGraphics.pm  1.30  6 years  golsen  Minor changes due to redefinitions. Add "no warnings qw( redefine );"
GenomeCodonUsages.pm  1.3  6 years  golsen  Very minor changes.
GenomeIDMap.pm  1.4  13 years  olson  Added license words.
GenomeLists.pm  1.2  11 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
GenomeMeta.pm  1.16  9 years  olson  Add lock retries; probably not needed now that I think I've fixed FileLocking bu...
GenomeMetaDB.pm  1.5  10 years  jared  added update_path
GenomeMetaDatabase.pm  1.1  10 years  jared  *** empty log message ***
GenomeSelector.pm  1.3  6 years  golsen  Fix the case of the directory with the JavaScript.
GenomeTypeObject.pm  1.18  5 years  olson  write to alternate assigned_functions file if presented in options
HTML.pm  1.137  6 years  golsen  Add a <META html-equiv...> tag in <HEAD>
HTML.py  1.6  13 years  olson  Added license words.
HtmlPageParser.pm  1.2  13 years  olson  Added license words.
IDclient.pm  1.2  5 years  olson  Modifications for new RAST2 services.
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
JobScheduler.pm  1.10  8 years  olson  Put. The Scheduler. Back.
KBRpcContext.pm  1.1  7 years  olson  KB context object for RPC support.
KBaseCodonUsage.pm  1.1  6 years  golsen  They sort of speak for themselves. Make packages with uniform calling convention...
KGML.pm  1.4  12 years  olson  Hope college modifications.
KGMLData.pm  1.5  6 years  redwards  Removing the defined(%hash) is deprecated and defined(@array) is deprecated warn...
KmerClassifier.pm  1.2  5 years  olson  add sas decl
KmerClient.pm  1.2  5 years  olson  Ensure the module still loads if genome map load fails.
KmerMgr.pm  1.6  6 years  olson  add sas tag
Kmers.pm  1.40  5 years  olson  add neighbor computation code.
Kmers2013.pm  1.1  6 years  disz  new kmer modules
KmersOld.pm  1.1  9 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
LinksUI.pm  1.20  7 years  overbeek  try to pass user correctly
ListServerScripts.pm  1.2  8 years  parrello  Fixed to point to PUBSEED server for documentation.
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
MD5Computer.pm  1.5  6 years  parrello  Sapling fixes.
MSSeedSupport.pm  1.1  8 years  devoid  Adding MSSeedSupport, a SVR package for ModelSEED to support genomes from RAST.
Makefile  1.15  6 years  olson  Changes from pangenome work.
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
Markups.pm  1.2  11 years  parrello  Changed POD format for better compatability with Wiki.
MergeTransactions.pm  1.3  11 years  parrello  Changed POD format for better compatability with Wiki.
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
MgRastSims.pm  1.1  10 years  redwards  a new package for getting sims for the mg-rast
MinimalTracer.pm  1.1  9 years  olson  More FS_RAST modes & supporting code for SAS use.
NCBI_genetic_code.pm  1.4  7 years  golsen  Add start codons to genetic code data.
NCBI_taxonomy.pm  1.5  6 years  golsen  Fix code to match current return from NCBI.
NRTools.pm  1.4  10 years  olson  update to new metadata standard
NewGenome.pm  1.82  7 years  gdpusch  Fixed 0 == undef bug on contig IDs.
Observation.pm  1.83  8 years  redwards  correcting web links
OddStarts_ref.pm  1.1  11 years  overbeek  add the ability to find TIF3
Overlap.pm  1.4  11 years  parrello  Changed POD format for better compatability with Wiki.
P2P.pm  1.31  13 years  olson  Added license words.
P2Pupdate.pm  1.64  8 years  olson  Fix indexing upon subsystem installation
PG.pm  1.8  6 years  overbeek  handle extraction of genome ids better
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
PageBuilder.pm  1.15  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
ParalogResolution.pm  1.6  8 years  golsen  Add a fraction identity filter of finding paralogs.
PartitionSeqs.pm  1.3  10 years  overbeek  return either scalar or list
PersistentSets.pm  1.3  8 years  disz  filled in all functions
Phage.pm  1.4  6 years  redwards  adding phage stuff
PickFeatureSet.pm  1.2  10 years  overbeek  add .html to HTML files
PinnedRegions.pm  1.40  5 years  olson  Add support for kmer-based pin detection.
Prodigal.pm  1.6  5 years  olson  add diag to when rmtree $tmpdir fails
ProtFamLite.pm  1.2  10 years  arodri7  added functions and made functions work
ProtFams.pm  1.3  10 years  arodri7  added functions and made functions work
ProtFamsLite.pm  1.2  10 years  arodri7  added functions and made functions work
ProtSims.pm  1.20  8 years  gdpusch  Turn off the annoying and confusing "Blat returns 0" diagnostic message unless $...
Prot_reps_drug_resistance.pm  1.2  5 years  golsen  Fixed spelling of $max_exptrapolate to be $max_extrapolate. The value is exporte...
Quality.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
RAST_submission.pm  1.34  6 years  olson  bugfix
RASTserver.pm  1.25  6 years  redwards  Adding the ability to get users jobs
RC.pm  1.33  7 years  disz  FIxed genome_data call
README  1.1.1.1  15 years  efrank   import
RNA_reps_5S_rRNA.pm  1.5  5 years  olson  make sas components.
RNA_reps_LSU_rRNA.pm  1.5  5 years  olson  make sas components.
RNA_reps_SSU_rRNA.pm  1.5  5 years  olson  make sas components.
ReactionPath.pm  1.1  8 years  parrello  Added new method to compute reaction paths.
RemoteCustomAttributes.pm  1.8  11 years  parrello  Changed POD format for better compatability with Wiki.
RiboProtQC.pm  1.2  6 years  fangfang  fix bug in detecting genomes with duplicated ribo proteins
RoleRule.pm  1.1  8 years  parrello  New modules for analyzing protein family functions.
RoleRuleSubstring.pm  1.1  8 years  parrello  New modules for analyzing protein family functions.
SAP.pm  1.190  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
SAPserver.pm  1.14  8 years  parrello  Support for local SQLite servers.
SAPtutorial.pm  1.10  9 years  parrello  Fixed some errors in examples of ID types.
SEED.spec  1.3  6 years  olson  Add get_genome_features
SEEDClient.pm  1.3  6 years  olson  Add get_genome_features
SEEDImpl.pm  1.4  6 years  olson  Add get_genome_features
SEEDServer.pm  1.3  6 years  olson  Add get_genome_features
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
SS.pm  1.13  9 years  parrello  More documentation cleanup.
SSU_rRNA_reps.pm  1.5  6 years  golsen  Add note indicating that this is now depricated. use RNA_rep_SSU_rRNA
SSserver.pm  1.17  9 years  parrello  Removed from the SAS distribution.
SUP.pm  1.3  7 years  parrello  Removed obsolete alignment stuff.
SUPserver.pm  1.1  9 years  parrello  New Sapling update support.
SameFunc.pm  1.17  11 years  overbeek  fix to SameFunc.pm
SampleDir.pm  1.4  9 years  olson  More analysis fixes; user-agent setting.
SapCompareRegions.pm  1.6  5 years  olson  Use the local SEED's FIG::sims if possible to retrieve sims; this will enable re...
SaplingAlignmentPsiBLAST.pm  1.1  5 years  golsen  A package to find best matches of sequences in a database to sequences in an ali...
SaplingCodonUsage.pm  1.1  6 years  golsen  They sort of speak for themselves. Make packages with uniform calling convention...
SaplingGenomeData.pm  1.3  6 years  fangfang  fix bug in all_genome_peg_data()
Scenario.pm  1.10  8 years  dejongh  change scenario handling to use path_info.txt
ScriptThing.pm  1.8  9 years  parrello  Expression vector support methods.
SeedAlignAndTreeToKBase.pm  1.7  7 years  fangfang  Remove the superseded_by column for both Alignment.tab and Tree.tab to match the...
SeedAware.pm  1.19  6 years  olson  fix system_with_redirect for use with fcgi
SeedCodonUsage.pm  1.2  6 years  golsen  Significant clean-up.
SeedCodonUsageToKBase.pm  1.1  7 years  golsen  Build files to support moving codon usage data into KBase.
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
SeedEnv.pm  1.5  5 years  olson  Make conditional on existence of ModelSEED.
SeedHTML.pm  1.3  9 years  olson  More distro fixes.
SeedSearch.pm  1.4  7 years  olson  add new type
SeedSims.pm  1.1  10 years  overbeek  additions to support partitioning of sims
SeedUtils.pm  1.71  5 years  overbeek  add Kbase to genome_of
SeedV.pm  1.10  8 years  olson  fix nasty boundary bug
SeqStore.pm  1.1  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
ServComplex.pm  1.6  7 years  overbeek  fixes to make Sapling version work
ServFIGfam.pm  1.7  7 years  overbeek  minor changes
ServFeature.pm  1.24  7 years  overbeek  allow updates
ServGenome.pm  1.15  7 years  overbeek  pass user
ServIndex.pm  1.2  7 years  overbeek  starting to work
ServOTU.pm  1.8  7 years  overbeek  minor fixes
ServReaction.pm  1.5  7 years  overbeek  fixes
ServRole.pm  1.5  7 years  overbeek  fixes to make Sapling version work
ServSubsysRow.pm  1.11  7 years  overbeek  minor fixes
ServerScripts.pm  1.5  9 years  overbeek  add summarize_MG_output
ServerThing.pm  1.90  7 years  olson  Add metabolic_reconstruction to the list of commands sent to the slow queue.
Signatures.pm  1.2  9 years  parrello  Various POD fixes.
Sim.pm  1.17  7 years  golsen  Fix duplicate defintion of new(). Add usage().
Sim2.pm  1.1  8 years  overbeek  tree sims
SimFC.pm  1.3  10 years  overbeek  handle deleted FIDs and failure to get translations
SimsTable.pm  1.11  6 years  golsen  Work around an issue when a user-supplied blast query has a fig| id that is not ...
SproutFIG.pm  1.10  13 years  olson  Added license words.
SproutSearch.pm  1.11  13 years  olson  Added license words.
StandaloneSims.pm  1.1  11 years  olson  FIGM/FIGV changes for sims between RAST orgs.
Stats.pm  1.10  7 years  parrello  KBase changes and C-based YAML.
StrepRepeats.pm  1.2  5 years  olson  add raw-repeats method
Subsystem.pm  1.154  8 years  olson  forgot the delete on subsystem_nonaux_role
SubsystemPrimer.pm  1.8  8 years  overbeek  better help
SubsystemPrimer2SS.pm  1.2  7 years  overbeek  update index
TBLstuff.pm  1.2  10 years  overbeek  minor fixes
TableCell.pm  1.1  7 years  golsen  Support for a new sims table format.
TemplateObject.pm  1.8  11 years  parrello  Changed POD format for better compatability with Wiki.
TestUtils.pm  1.12  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
ToCall.pm  1.12  8 years  gdpusch  Modified to allow FIGfam IDs with arbitrarily many digits, and to fail safe if F...
Tracer.pm  1.137  5 years  olson  Don't change $FIG_Config::temp
TransactionProcessor.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
TreeFC.pm  1.1  6 years  fangfang  Add module for tree-based functional coupling.
UnvSubsys.pm  1.20  11 years  paczian  added missing "use HTML;"
UpdateServer.pm  1.2  7 years  disz  Remove Sapling stuff`
UserDB.pm  1.2  13 years  olson  Added license words.
UserData.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
WebColors.pm  1.16  8 years  paczian  re-added circle color scheme
WikiTools.pm  1.8  10 years  parrello  Fixed a glitch in list rendering.
WriteEMBL.pm  1.1  8 years  gdpusch  Initial checkin --- probably still needs work.
WriteGenbank.pm  1.2  8 years  gdpusch  Forgot trailing "1;" :(
__init__.py  1.2  13 years  olson  Added license words.
align_and_tree_test.pm  1.1  8 years  golsen  Temp code for using DBMS version of alignment and tree access.
bidir_best_hits.pm  1.1  7 years  golsen  Code for bidirectional best hits in a form used by codon usage analysis software...
clustaltree.pm  1.3  10 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
collect_related_sequences.pm  1.6  9 years  golsen  Update to use SeedAware.pm (and do some general clean-up).
compare_coding.pm  1.10  8 years  golsen  Integrate use of SeedAware.pm
crispr.pm  1.4  5 years  golsen  Fix bug in which $replen was overloaded, and not reinitialized.
display_related_genomes.pm  1.2  9 years  golsen  Minor documentation changes in code.
fastDNAml.pm  1.2  13 years  olson  Added license words.
ffxtree.pm  1.29  7 years  fangfang  add css colors
find_homologs.pm  1.10  5 years  olson  Remove unused references to FIG_Config. add sas directive to find_homologs.
find_special_proteins.pm  1.13  6 years  golsen  Change the temporary_directory function to be that in SeedAware.pm
gd_tree_0.pm  1.5  9 years  golsen  Extensive reworking of color management.
genome_frequencies.pm  1.3  7 years  golsen  Minor changes to GenomeCodonUsages.pm Add notice that genome_frequencies.pm will...
gjoalign2html.pm  1.11  7 years  golsen  Support for residue color = none.
gjoalignandtree.pm  1.20  6 years  golsen  Add more flexibility ot extract_with_psiblast. Fix most of the temporary file na...
gjoalignment.pm  1.43  5 years  golsen  Make add_to_alignment_v2() operate silently as default.
gjocodonlib.pm  1.11  5 years  golsen  Add Windows support for n_cpu().
gjocolorlib.pm  1.7  8 years  golsen  Added support for luma (HSY color definitions). Changed all code so that html co...
gjogenbank.pm  1.11  6 years  golsen  This module now emits a perl warning regarding $paranthetical. Just added some l...
gjogff.pm  1.2  8 years  golsen  Changes to fix some bugs in GenBank format reading and writing. Changes to deal ...
gjolib.pm  1.4  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
gjolists.pm  1.2  12 years  golsen  Updates for cleaner faster code.
gjonativecodonlib.pm  1.3  6 years  golsen  Significant reorganization to support data from alternative sources.
gjonewicklib.pm  1.33  6 years  fangfang  add an option in representative_tips
gjoparseblast.pm  1.11  5 years  golsen  Slightly cleaner version of splitting sequence id and definition.
gjophylip.pm  1.9  8 years  golsen  Fix a cosmetic issue in the cleaning of sequences for PHYLIP.
gjosegmentlib.pm  1.2  8 years  golsen  Forgot the SAS component lines.
gjoseqlib.pm  1.34  5 years  golsen  fix an error in interpret_aa_alignment().
gjostat.pm  1.5  5 years  olson  Add SAS header.
high_expression_ref_ab.pm  1.1  7 years  golsen  Additional data for codon usage analyses.
match_to_axes.pm  1.3  6 years  golsen  A more radical solution to making this module obsolete. Use CodonUsageTable.pm i...
model.pm  1.36  8 years  dejongh  change scenario handling to use path_info.txt
overlap_resolution.pm  1.5  5 years  golsen  Some code clean up and better use of pre-existing feature priority.
proml.pm  1.10  6 years  golsen  Change tempoary file names and locations to be more robust.
protdist_neighbor.pm  1.2  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
pyrrolysylprotein_ref_seq.pm  1.2  7 years  olson  Make these SAS components
raedraw.pm  1.14  11 years  parrello  Changed POD heading levels.
raelib.pm  1.47  6 years  redwards  adding phage stuff
representative_sequences.pm  1.22  6 years  golsen  Some minor improvements in code and documentations (comments).
selenoprotein_ref_seq.pm  1.7  7 years  olson  Make these SAS components
set_utilities.pm  1.3  9 years  overbeek  make SAS components
tree_neighborhood.pm  1.1  12 years  overbeek  add tree_neighbors and latest phylogeny stuff
tree_utilities.pm  1.21  6 years  overbeek  null label is empty string

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