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ProtSims.pm  1.22  6 days  gdpusch  Fixed a debug message that has been confusing me for years.
FIG.pm  1.936  6 days  gdpusch  Deleted a spurious comment that was just a note to myself
SimCompute.pm  1.1  6 weeks  olson  Little Dancer app to handle serving up data chunks for sims compute and uploadin...
Subsystem.pm  1.157  4 months  olson  Fix perf bug where we query database many times just to find version info. This ...
AlignsAndTreesServer.pm  1.30  4 months  olson  If a $ReferenceFIG is set, use that for md5/peg mapping lookups instead of sapli...
GEO.pm  1.4  4 months  parrello  Updates from SEEDtk
EvalCom.pm  1.2  4 months  parrello  Changes from SEEDtk
GenBankToGTO.pm  1.5  5 months  olson  Fix undefind to undefined Add details from assembly gap feature data
TabFile.pm  1.1  5 months  parrello  Changes copied from SEEDtk project.
P3Signatures.pm  1.8  5 months  parrello  Changes copied from SEEDtk project.
pubmed.tt  1.1  5 months  parrello  Changes copied from SEEDtk project.
FastA.pm  1.5  5 months  parrello  Changes copied from SEEDtk project.
P3Utils.pm  1.20  5 months  parrello  Changes copied from SEEDtk project.
BinningReports.pm  1.3  5 months  parrello  Changes copied from SEEDtk project.
GPUtils.pm  1.3  5 months  parrello  Changes copied from SEEDtk project.
P3Sequences.pm  1.1  5 months  parrello  Changes copied from SEEDtk project.
SeedUtils.pm  1.93  5 months  parrello  Changes copied from SEEDtk project.
RASTlib.pm  1.10  5 months  parrello  Changes copied from SEEDtk project.
KmerDb.pm  1.9  5 months  parrello  Changes copied from SEEDtk project.
RepGenome.pm  1.1  5 months  parrello  Changes copied from SEEDtk project.
P3DataAPI.pm  1.35  5 months  parrello  Changes copied from SEEDtk project.
CloseStrains.pm  1.32  5 months  gdpusch  Corrected typo in the description of columns 6 and 7 of the "Signature Output" t...
NCBI_genetic_code.pm  1.7  7 months  gdpusch  Added genetic codes 24 through 33.
Prodigal.pm  1.10  7 months  olson  Add support for finding and logging full path and version information.
EvalHelper.pm  1.3  10 months  parrello  Changes copied from SEEDtk project.
FastQ.pm  1.4  11 months  parrello  Changes copied from SEEDtk project.
GenomeChecker.pm  1.2  11 months  parrello  Changes copied from SEEDtk project.
IC50.pm  1.3  11 months  parrello  Changes copied from SEEDtk project.
Contigs.pm  1.8  11 months  parrello  Changes copied from SEEDtk project.
EvalCon.pm  1.2  11 months  parrello  Changes copied from SEEDtk project.
RoleParse.pm  1.3  11 months  parrello  Changes copied from SEEDtk project.
SRAlib.pm  1.3  11 months  parrello  Changes copied from SEEDtk project.
GenomeTypeObject.pm  1.46  12 months  olson  Merge bob version
StrepRepeats.pm  1.4  12 months  olson  Break KBase dependency
SubsystemProjector.pm  1.3  12 months  parrello  Changes copied from SEEDtk project.
Category.pm  1.1  12 months  parrello  Changes copied from SEEDtk project.
Bin.pm  1.1  12 months  parrello  Changes copied from SEEDtk project.
BasicLocation.pm  1.31  12 months  parrello  Changes copied from SEEDtk project.
Hsp.pm  1.3  12 months  parrello  Changes copied from SEEDtk project.
tree_utilities.pm  1.25  12 months  parrello  Changes copied from SEEDtk project.
set_utilities.pm  1.4  12 months  parrello  Changes copied from SEEDtk project.
gjocluster.pm  1.2  14 months  golsen  Fix package loading inside an eval.
gjocontigmap.pm  1.1  14 months  golsen  Some utilities for quickly finding features in a region of a contig. It is a wo...
ScriptUtils.pm  1.7  18 months  parrello  Changes copied from SEEDtk project.
BlastInterface.pm  1.29  18 months  olson  Where possible, use File::Spec->devnull to determine null device. It's different...
ServicesUtils.pm  1.8  18 months  olson  Add SAS header.
TaxUtils.pm  1.1  20 months  gdpusch  Initial checkin of taxonomic-Kmer modules.
PredictTaxonID.pm  1.1  20 months  gdpusch  Initial checkin of taxonomic-Kmer modules.
TetraMap.pm  1.1  22 months  parrello  Changes copied from SEEDtk project.
TetraProfile.pm  1.1  22 months  parrello  Changes copied from SEEDtk project.
P3Contigs.pm  1.1  22 months  parrello  Changes copied from SEEDtk project.
overlap_resolution.pm  1.9  23 months  olson  Fix score and qual check for seleno/pyrrolysoproteins.
crispr.pm  1.10  2 years  parrello  Changes copied from SEEDtk project.
SeedDas.pm  1.23  2 years  olson  fix deprecated regular expression syntax
AminoAcidMatrix.pm  1.1  2 years  golsen  Tools for handling amino acid scoring matrices. Has many matrices built-in. Prov...
NCBI_taxonomy.pm  1.6  2 years  golsen  Changed to https.
gjocontigs.pm  1.1  2 years  golsen  A new package defining a contigs object that provides random access to DNA seque...
gjoseqlib.pm  1.48  2 years  golsen  Several new functions, and added cleaner names for a few commonly used functions...
gjogenbank.pm  1.17  2 years  golsen  A few new access functions. Some clarifications.
NCBI_sequence.pm  1.2  2 years  golsen  Fix the URL to be https Add flexibility to format of a list of ids.
gjoalignment.pm  1.52  2 years  golsen  Added some more functions. Added a cluster option to representative alignment to...
SeedSearch.pm  1.7  2 years  olson  add crispr_array to indexed types list
TraceObject.pm  1.1  2 years  parrello  Changes copied from SEEDtk project.
P3WorkspaceClient.pm  1.6  2 years  parrello  Changes copied from SEEDtk project.
CallByProjection.pm  1.5  2 years  olson  Remove hopefully unused dependencies.
FQUtils.pm  1.1  2 years  parrello  Changes copied from SEEDtk project.
Nov_2016_AMR_Classifiers.pm  1.2  2 years  jdavis  Added Klebsiella classifiers
Boolean.pm  1.4  2 years  overbeek  fix tree_utilities parser
AdaboostClassify.pm  1.4  2 years  olson  Move to Nov_2016_AMR_Classifiers classifier module. Adds required changes to bla...
PinnedRegions.pm  1.42  3 years  olson  Add more pattyfam support.
SwissProtUtils.pm  1.1  3 years  golsen  Utilities for converting Swiss-Prot XML to JSON, reading the JSON, and extractin...
Kmers.pm  1.42  3 years  olson  Remove duplicated FIG object creation.
RAST_submission.pm  1.37  3 years  olson  Add rasttk submission support
KBInvoke.pm  1.1  3 years  olson  Simple KBase-style RPC invocation module. Includes PATRIC/RAST/KBase login funct...
find_tRNAs.pm  1.1  3 years  golsen  The beginnings of an interface to tRNAscan-SE, with functions for fixing issues ...
ClusterPairs.pm  1.1  3 years  parrello  Changes copied from SEEDtk project.
PropagateGBMetadata.pm  1.3  3 years  olson  Adjust interval tree endpoint.
MissingRoles.pm  1.1  3 years  parrello  Changes copied from SEEDtk project.
AdaboostClassifierAMRv1.pm  1.1  3 years  olson  Jim Davis' classifier code.
ANNO.pm  1.14  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
FIGV.pm  1.105  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
WriteEMBL.pm  1.2  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
gjogff.pm  1.3  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
ANNOserver.pm  1.27  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
SeedV.pm  1.11  3 years  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
find_special_proteins.pm  1.15  3 years  golsen  Add a few more data to the returned data on matches, and documented.
KmerRepGenomes.pm  1.4  3 years  parrello  Changes copied from SEEDtk project.
AlignTree.pm  1.53  3 years  fangfang  remove empty sequences in trimmed alignments
KmerGutsNet.pm  1.2  3 years  olson  add sas
SEEDServer.pm  1.4  3 years  olson  Add get_genomes() to the SEED RPC API.
SEED.spec  1.4  3 years  olson  Add get_genomes() to the SEED RPC API.
SEEDImpl.pm  1.5  3 years  olson  Add get_genomes() to the SEED RPC API.
SEEDClient.pm  1.5  3 years  olson  Add get_genomes() to the SEED RPC API.
IDclient.pm  1.6  3 years  parrello  Changes copied from SEEDtk project.
Sim.pm  1.19  3 years  parrello  Changes copied from SEEDtk project.
GenomeMeta.pm  1.19  3 years  olson  Add missing module.
SaplingAlignmentPsiBLAST.pm  1.3  3 years  golsen  Start adding support for extracting specific sequence positions based upon the a...
CodonUsageTable.pm  1.6  3 years  golsen  Add ability to dynamically change links to alternative SEEDs. Other minor clean-...
bidir_best_hits.pm  1.3  3 years  golsen  Fix temp file handling to get rid of warning of unsafe usage. The clean up of th...
display_related_genomes.pm  1.3  3 years  golsen  Add an alternative function call that is much simpler and cleaner.
ParseSIBEnzyme.pm  1.1  4 years  redwards  module and scripts to compare EC numbers to what we have in the SEED
SeedCodonUsage.pm  1.4  4 years  golsen  Fix typo in the documentation.
Stats.pm  1.12  4 years  parrello  Changes copied from SEEDtk project.
ConservedDomainSearch.pm  1.4  4 years  olson  Bulk lookups. More feature generation fixes.
MD5Computer.pm  1.8  4 years  parrello  Fixed an error in ProcessContig.
SeedURLs.pm  1.2  4 years  parrello  Fixed spacing.
ScriptThing.pm  1.9  4 years  parrello  Changes copied from SEEDtk project.
Biochemistry.pm  1.4  4 years  overbeek  fixes for reactions
Observation.pm  1.84  4 years  redwards  removing defined @ which is deprecated and throws an error
Universal_Seqs.pm  1.1  4 years  jdavis  perl module for finding universal proteins from a peer bork paper
MapToRef.pm  1.2  4 years  parrello  Changes copied from SEEDtk project.
BBasicLocation.pm  1.2  4 years  parrello  Changes copied from SEEDtk project.
FBasicLocation.pm  1.2  4 years  parrello  Changes copied from SEEDtk project.
find_homologs.pm  1.11  4 years  golsen  Make blast+ the default in find_nucleotide_homologs, solving an issue with occas...
DBKernel.pm  1.83  4 years  parrello  Added support for IGNORE and REPLACE in load_table.
Find_RNAs.pm  1.6  4 years  olson  Fix shell escape bug.
RASTserver.pm  1.26  4 years  olson  Add proxy support.
gjonativecodonlib.pm  1.4  4 years  golsen  Fix the logic so that codon count files created by native_codon_usage() do not g...
gjocodonlib.pm  1.13  4 years  golsen  Fix the logic so that codon count files created by native_codon_usage() do not g...
Tpn_Int_Reps.pm  1.2  5 years  olson  add sas tag
IS_Subroutines.pm  1.3  5 years  olson  Fixes for IS.
IS_Data.pm  1.2  5 years  olson  Fixes for IS.
ffxtree.pm  1.31  5 years  fangfang  update raxml
SaplingCodonUsage.pm  1.2  5 years  golsen  Increased functionality. Improved documentation.
KBaseCodonUsage.pm  1.2  5 years  golsen  Code clean up. Improved documentation. Some increased functionality.
gjostat.pm  1.6  5 years  golsen  Add more error checking and a median routine.
gjoavllib.pm  1.1  5 years  golsen  Some support for clustering and generating representatives of an alignment at an...
GenomeSetClient.pm  1.1  5 years  olson  New genome set stuff.
GenomeSetServer.pm  1.1  5 years  olson  New genome set stuff.
GenomeSet.spec  1.1  5 years  olson  New genome set stuff.
GenomeSetImpl.pm  1.1  5 years  olson  New genome set stuff.
ClientThing.pm  1.32  5 years  parrello  Added support for Core Sapling server.
FIGM.pm  1.22  5 years  olson  Rollup of RASTtk changes.
FFs.pm  1.58  5 years  olson  Tie the translation btree.
Tracer.pm  1.137  5 years  olson  Don't change $FIG_Config::temp
SapCompareRegions.pm  1.6  5 years  olson  Use the local SEED's FIG::sims if possible to retrieve sims; this will enable re...
SeqStore.pm  1.1  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
SAP.pm  1.190  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
KmerClient.pm  1.2  5 years  olson  Ensure the module still loads if genome map load fails.
Clearinghouse.pm  1.7  5 years  olson  Don't spit output to stdout.
SeedEnv.pm  1.5  5 years  olson  Make conditional on existence of ModelSEED.
KmerClassifier.pm  1.2  5 years  olson  add sas decl
RNA_reps_LSU_rRNA.pm  1.5  5 years  olson  make sas components.
RNA_reps_5S_rRNA.pm  1.5  5 years  olson  make sas components.
RNA_reps_SSU_rRNA.pm  1.5  5 years  olson  make sas components.
Prot_reps_drug_resistance.pm  1.2  5 years  golsen  Fixed spelling of $max_exptrapolate to be $max_extrapolate. The value is exporte...
gjoparseblast.pm  1.11  5 years  golsen  Slightly cleaner version of splitting sequence id and definition.
CrossSeedLinks.pm  1.1  5 years  golsen  Rudimentary support for links between SEEDs. Nothing currenly uses it, but it se...
Diagram.pm  1.22  5 years  seaver  Removing STDERR debug statements from Diagram.pm
DrugResistanceDB.pm  1.1  5 years  overbeek  drug resistance reps db
SimsTable.pm  1.11  5 years  golsen  Work around an issue when a user-supplied blast query has a fig| id that is not ...
gjonewicklib.pm  1.33  5 years  fangfang  add an option in representative_tips
RiboProtQC.pm  1.2  5 years  fangfang  fix bug in detecting genomes with duplicated ribo proteins
GenomeSelector.pm  1.3  5 years  golsen  Fix the case of the directory with the JavaScript.
SeedAware.pm  1.19  5 years  olson  fix system_with_redirect for use with fcgi
HTML.pm  1.137  5 years  golsen  Add a <META html-equiv...> tag in <HEAD>
SSU_rRNA_reps.pm  1.5  6 years  golsen  Add note indicating that this is now depricated. use RNA_rep_SSU_rRNA
PG.pm  1.8  6 years  overbeek  handle extraction of genome ids better
KmerMgr.pm  1.6  6 years  olson  add sas tag
FF.pm  1.36  6 years  olson  Add SAS declarations.
Dlits.pm  1.6  6 years  olson  Catch bad pmids so db call doesn't crash.
SaplingGenomeData.pm  1.3  6 years  fangfang  fix bug in all_genome_peg_data()
TreeFC.pm  1.1  6 years  fangfang  Add module for tree-based functional coupling.
KGMLData.pm  1.5  6 years  redwards  Removing the defined(%hash) is deprecated and defined(@array) is deprecated warn...
Phage.pm  1.4  6 years  redwards  adding phage stuff
raelib.pm  1.47  6 years  redwards  adding phage stuff
Makefile  1.15  6 years  olson  Changes from pangenome work.
Cmd2HTML.pm  1.11  6 years  overbeek  add compound_to_reactions
FC.pm  1.22  6 years  parrello  Fixed to improve performance of pairset deletions.
GenomeCodonUsages.pm  1.3  6 years  golsen  Very minor changes.
CommonCGI.pm  1.1  6 years  olson  common cgi code.
gjoalignandtree.pm  1.20  6 years  golsen  Add more flexibility ot extract_with_psiblast. Fix most of the temporary file na...
GenerateClusters.pm  1.2  6 years  overbeek  require % iden >= 50 for projection: UNTESTED
Kmers2013.pm  1.1  6 years  disz  new kmer modules
FIGStatisticalModels.pm  1.8  6 years  gdpusch  mean() modified to use round-off-protected Kahan summation. stdev() modified to ...
GenoGraphics.pm  1.30  6 years  golsen  Minor changes due to redefinitions. Add "no warnings qw( redefine );"
representative_sequences.pm  1.22  6 years  golsen  Some minor improvements in code and documentations (comments).
match_to_axes.pm  1.3  6 years  golsen  A more radical solution to making this module obsolete. Use CodonUsageTable.pm i...
proml.pm  1.10  6 years  golsen  Change tempoary file names and locations to be more robust.
CGIAlignTreeViewer.pm  1.24  6 years  golsen  Convert image files to use new temporary file name functions.
ServerThing.pm  1.90  6 years  olson  Add metabolic_reconstruction to the list of commands sent to the slow queue.
ALITRE.pm  1.6  6 years  fangfang  add server side implementation of alignments_metadata_by_md5() and alignment...
AlignsAndTrees.pm  1.17  6 years  fangfang  add server side implementation of alignments_metadata_by_md5() and alignment...
genome_frequencies.pm  1.3  7 years  golsen  Minor changes to GenomeCodonUsages.pm Add notice that genome_frequencies.pm will...
SeedCodonUsageToKBase.pm  1.1  7 years  golsen  Build files to support moving codon usage data into KBase.
SeedAlignAndTreeToKBase.pm  1.7  7 years  fangfang  Remove the superseded_by column for both Alignment.tab and Tree.tab to match the...
gjoalign2html.pm  1.11  7 years  golsen  Support for residue color = none.
selenoprotein_ref_seq.pm  1.7  7 years  olson  Make these SAS components
pyrrolysylprotein_ref_seq.pm  1.2  7 years  olson  Make these SAS components
CloseGenomes.pm  1.2  7 years  olson  add sas tag
FS_RAST.pm  1.39  7 years  overbeek  fix default of genetic code
high_expression_ref_ab.pm  1.1  7 years  golsen  Additional data for codon usage analyses.
RC.pm  1.33  7 years  disz  FIxed genome_data call
AliasAnalysis.pm  1.13  7 years  parrello  Added IMG and ERIC.
Corresponds.pm  1.1  7 years  overbeek  finally debugged
ServFeature.pm  1.24  7 years  overbeek  allow updates
ServGenome.pm  1.15  7 years  overbeek  pass user
LinksUI.pm  1.20  7 years  overbeek  try to pass user correctly
UpdateServer.pm  1.2  7 years  disz  Remove Sapling stuff`
ServOTU.pm  1.8  7 years  overbeek  minor fixes
ServFIGfam.pm  1.7  7 years  overbeek  minor changes
ServReaction.pm  1.5  7 years  overbeek  fixes
ServSubsysRow.pm  1.11  7 years  overbeek  minor fixes
ServIndex.pm  1.2  7 years  overbeek  starting to work
ServRole.pm  1.5  7 years  overbeek  fixes to make Sapling version work
ServComplex.pm  1.6  7 years  overbeek  fixes to make Sapling version work
NewGenome.pm  1.82  7 years  gdpusch  Fixed 0 == undef bug on contig IDs.
SubsystemPrimer2SS.pm  1.2  7 years  overbeek  update index
FFB3.pm  1.1  7 years  olson  figfam build helper module
KBRpcContext.pm  1.1  7 years  olson  KB context object for RPC support.
Clearinghouse.py  1.12  7 years  olson  Use new SS clearinghouse on pubseed.
SUP.pm  1.3  7 years  parrello  Removed obsolete alignment stuff.
TableCell.pm  1.1  7 years  golsen  Support for a new sims table format.
AliTreeSims.pm  1.8  7 years  fangfang  fixed a variable name
BlankSVP.pm  1.1  7 years  olson  Script & infrastructure for creating easy seedviewer pages.
FIGgjo.pm  1.5  7 years  golsen  Support for better role coloring and formatting.
ExpressionDir.pm  1.12  7 years  olson  add compute_pearson_corr
MSSeedSupport.pm  1.1  7 years  devoid  Adding MSSeedSupport, a SVR package for ModelSEED to support genomes from RAST.
PersistentSets.pm  1.3  8 years  disz  filled in all functions
SubsystemPrimer.pm  1.8  8 years  overbeek  better help
FBAMODELserver.pm  1.5  8 years  chenry  Moving FBAMODELserver.pm to FigKernelPackages, and changing URL.
gjolib.pm  1.4  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
protdist_neighbor.pm  1.2  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
ParalogResolution.pm  1.6  8 years  golsen  Add a fraction identity filter of finding paralogs.
ToCall.pm  1.12  8 years  gdpusch  Modified to allow FIGfam IDs with arbitrarily many digits, and to fail safe if F...
PageBuilder.pm  1.15  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
TestUtils.pm  1.12  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
FIGRules.pm  1.56  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
ChromosomalClusters.pm  1.11  8 years  parrello  Added "roles_to_proteins" method.
P2Pupdate.pm  1.64  8 years  olson  Fix indexing upon subsystem installation
CorrTableEntry.pm  1.5  8 years  overbeek  add 20th column - clear_bbhs
align_and_tree_test.pm  1.1  8 years  golsen  Temp code for using DBMS version of alignment and tree access.
RoleRuleSubstring.pm  1.1  8 years  parrello  New modules for analyzing protein family functions.
RoleRule.pm  1.1  8 years  parrello  New modules for analyzing protein family functions.
ReactionPath.pm  1.1  8 years  parrello  Added new method to compute reaction paths.
ALITREserver.pm  1.1  8 years  parrello  New alignment/tree server stuff.
ListServerScripts.pm  1.2  8 years  parrello  Fixed to point to PUBSEED server for documentation.
AliTreeIdConvert.pm  1.1  8 years  golsen  Functions for interconverting MD5 and peg ids of alignments and trees in the SEE...
JobScheduler.pm  1.10  8 years  olson  Put. The Scheduler. Back.
Sim2.pm  1.1  8 years  overbeek  tree sims
AT.pm  1.6  8 years  fangfang  add blast function
WebColors.pm  1.16  8 years  paczian  re-added circle color scheme
CorrespondenceCache.pm  1.2  8 years  parrello  Added experiment filter to "fid_experiments". Fixed correspondence cache to work...
gjosegmentlib.pm  1.2  8 years  golsen  Forgot the SAS component lines.
WriteGenbank.pm  1.2  8 years  gdpusch  Forgot trailing "1;" :(
gjophylip.pm  1.9  8 years  golsen  Fix a cosmetic issue in the cleaning of sequences for PHYLIP.
compare_coding.pm  1.10  8 years  golsen  Integrate use of SeedAware.pm
model.pm  1.36  8 years  dejongh  change scenario handling to use path_info.txt
Scenario.pm  1.10  8 years  dejongh  change scenario handling to use path_info.txt
SAPserver.pm  1.14  8 years  parrello  Support for local SQLite servers.
gjocolorlib.pm  1.7  8 years  golsen  Added support for luma (HSY color definitions). Changed all code so that html co...
Correspondence.pm  1.4  8 years  overbeek  correct the identity check
ATserver.pm  1.2  8 years  fangfang  default url set to biobig
Clustering.pm  1.6  8 years  overbeek  added double and triple linkage
SampleDir.pm  1.4  8 years  olson  More analysis fixes; user-agent setting.
SUPserver.pm  1.1  8 years  parrello  New Sapling update support.
BerkTable.pm  1.2  9 years  olson  fix arg
MinimalTracer.pm  1.1  9 years  olson  More FS_RAST modes & supporting code for SAS use.
Signatures.pm  1.2  9 years  parrello  Various POD fixes.
collect_related_sequences.pm  1.6  9 years  golsen  Update to use SeedAware.pm (and do some general clean-up).
FileLocking.pm  1.4  9 years  olson  Changes for DesktopRast. CVHnS: ------------------------------------------------...
ServerScripts.pm  1.5  9 years  overbeek  add summarize_MG_output
gd_tree_0.pm  1.5  9 years  golsen  Extensive reworking of color management.
ErrorMessage.pm  1.2  9 years  olson  remove unused use CGI.
SAPtutorial.pm  1.10  9 years  parrello  Fixed some errors in examples of ID types.
SeedHTML.pm  1.3  9 years  olson  More distro fixes.
SSserver.pm  1.17  9 years  parrello  Removed from the SAS distribution.
FFserver.pm  1.23  9 years  parrello  Removed from the SAS distribution.
ACHserver.pm  1.16  9 years  parrello  Removed from the SAS distribution.
COserver.pm  1.13  9 years  parrello  Removed from the SAS distribution.
KmersOld.pm  1.1  9 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
SS.pm  1.13  9 years  parrello  More documentation cleanup.
ACH.pm  1.7  9 years  disz  changed doc to say XXserver->new() insetad of XX->new
CO.pm  1.6  9 years  disz  changed doc to say XXserver->new() insetad of XX->new
FullLocation.pm  1.25  9 years  parrello  Added a method to compute the total location length.
GenomeMetaDatabase.pm  1.1  9 years  jared  *** empty log message ***
MgRastSims.pm  1.1  10 years  redwards  a new package for getting sims for the mg-rast
GenomeMetaDB.pm  1.5  10 years  jared  added update_path
DocUtils.pm  1.18  10 years  parrello  Added documentation functions to the Sapling server.
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
NRTools.pm  1.4  10 years  olson  update to new metadata standard
clustaltree.pm  1.3  10 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
PartitionSeqs.pm  1.3  10 years  overbeek  return either scalar or list
TBLstuff.pm  1.2  10 years  overbeek  minor fixes
AnnoClearinghouse.pm  1.44  10 years  wilke  Modified sql query to ? syntax
PickFeatureSet.pm  1.2  10 years  overbeek  add .html to HTML files
WikiTools.pm  1.8  10 years  parrello  Fixed a glitch in list rendering.
SimFC.pm  1.3  10 years  overbeek  handle deleted FIDs and failure to get translations
FIGAttributes.pm  1.4  10 years  overbeek  get rid of something
ProtFams.pm  1.3  10 years  arodri7  added functions and made functions work
ProtFamLite.pm  1.2  10 years  arodri7  added functions and made functions work
ProtFamsLite.pm  1.2  10 years  arodri7  added functions and made functions work
CompareMR.pm  1.8  10 years  paczian  cutting comments off of functional roles
SeedSims.pm  1.1  10 years  overbeek  additions to support partitioning of sims
OddStarts_ref.pm  1.1  10 years  overbeek  add the ability to find TIF3
StandaloneSims.pm  1.1  10 years  olson  FIGM/FIGV changes for sims between RAST orgs.
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
Assignments.pm  1.17  11 years  overbeek  remove impact of our annotations on making assignments using auto_assign
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
UnvSubsys.pm  1.20  11 years  paczian  added missing "use HTML;"
Blast.pm  1.5  11 years  overbeek  close TMP files in Blast.pm
raedraw.pm  1.14  11 years  parrello  Changed POD heading levels.
BadCall.pm  1.4  11 years  parrello  Replaced obsolete AddToListMap method.
Annotation.pm  1.4  11 years  parrello  Added a TITLE statement for the Wiki.
ButtonArray.pm  1.1  11 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
GenomeLists.pm  1.2  11 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
Quality.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
Overlap.pm  1.4  11 years  parrello  Changed POD format for better compatability with Wiki.
Markups.pm  1.2  11 years  parrello  Changed POD format for better compatability with Wiki.
TransactionProcessor.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
UserData.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
FudgeTransactions.pm  1.4  11 years  parrello  Changed POD format for better compatability with Wiki.
RemoteCustomAttributes.pm  1.8  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.
TemplateObject.pm  1.8  11 years  parrello  Changed POD format for better compatability with Wiki.
ApplyTransactions.pm  1.7  11 years  parrello  Changed POD format for better compatability with Wiki.
SameFunc.pm  1.17  11 years  overbeek  fix to SameFunc.pm
InsertIntoTree.pm  1.15  11 years  overbeek  check figfams fixes
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
KGML.pm  1.4  12 years  olson  Hope college modifications.
ContigMD5.pm  1.3  12 years  olson  clone the digest so that checksum() may be called multiple times
gjolists.pm  1.2  12 years  golsen  Updates for cleaner faster code.
tree_neighborhood.pm  1.1  12 years  overbeek  add tree_neighbors and latest phylogeny stuff
InterfaceRoutines.pm  1.12  12 years  olson  readonly fixes; seed-run-job update to run from input file
DBrtns.pm  1.27  13 years  overbeek  Fix extra-args option to go at teh start of the list.
Classes.pm  1.1  13 years  mkubal  added Organism class
COPYING.TXT  1.1  13 years  olson  add license file
__init__.py  1.2  13 years  olson  Added license words.
fastDNAml.pm  1.2  13 years  olson  Added license words.
GenomeIDMap.pm  1.4  13 years  olson  Added license words.
FIGrpc.pm  1.3  13 years  olson  Added license words.
P2P.pm  1.31  13 years  olson  Added license words.
FIGGenDB.pm  1.6  13 years  olson  Added license words.
SproutSearch.pm  1.11  13 years  olson  Added license words.
ClusterWorker.pm  1.2  13 years  olson  Added license words.
Construct.pm  1.2  13 years  olson  Added license words.
UserDB.pm  1.2  13 years  olson  Added license words.
FIGnet.pm  1.2  13 years  olson  Added license words.
HtmlPageParser.pm  1.2  13 years  olson  Added license words.
Cluster.pm  1.11  13 years  olson  Added license words.
FIGUtilities.pm  1.2  13 years  olson  Added license words.
FIG.py  1.13  13 years  olson  Added license words.
FIGtree.pm  1.3  13 years  olson  Added license words.
FIG2.py  1.2  13 years  olson  Added license words.
HTML.py  1.6  13 years  olson  Added license words.
SproutFIG.pm  1.10  13 years  olson  Added license words.
README  1.1.1.1  15 years  efrank   import

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