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Index of /FigKernelPackages

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File (rev) Rev. Age Author Last log entry
 Parent Directory        
tree_utilities.pm  1.21  6 years  overbeek  null label is empty string
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
set_utilities.pm  1.3  10 years  overbeek  make SAS components
selenoprotein_ref_seq.pm  1.7  7 years  olson  Make these SAS components
representative_sequences.pm  1.22  7 years  golsen  Some minor improvements in code and documentations (comments).
raelib.pm  1.47  6 years  redwards  adding phage stuff
raedraw.pm  1.14  12 years  parrello  Changed POD heading levels.
pyrrolysylprotein_ref_seq.pm  1.2  7 years  olson  Make these SAS components
protdist_neighbor.pm  1.2  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
proml.pm  1.10  7 years  golsen  Change tempoary file names and locations to be more robust.
overlap_resolution.pm  1.5  5 years  golsen  Some code clean up and better use of pre-existing feature priority.
model.pm  1.36  9 years  dejongh  change scenario handling to use path_info.txt
match_to_axes.pm  1.3  7 years  golsen  A more radical solution to making this module obsolete. Use CodonUsageTable.pm i...
high_expression_ref_ab.pm  1.1  7 years  golsen  Additional data for codon usage analyses.
gjostat.pm  1.6  5 years  golsen  Add more error checking and a median routine.
gjoseqlib.pm  1.38  5 years  golsen  Add sequence type guessing.
gjosegmentlib.pm  1.2  9 years  golsen  Forgot the SAS component lines.
gjophylip.pm  1.9  9 years  golsen  Fix a cosmetic issue in the cleaning of sequences for PHYLIP.
gjoparseblast.pm  1.11  6 years  golsen  Slightly cleaner version of splitting sequence id and definition.
gjonewicklib.pm  1.33  6 years  fangfang  add an option in representative_tips
gjonativecodonlib.pm  1.3  7 years  golsen  Significant reorganization to support data from alternative sources.
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
gjolib.pm  1.4  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
gjogff.pm  1.2  9 years  golsen  Changes to fix some bugs in GenBank format reading and writing. Changes to deal ...
gjogenbank.pm  1.11  7 years  golsen  This module now emits a perl warning regarding $paranthetical. Just added some l...
gjocolorlib.pm  1.7  9 years  golsen  Added support for luma (HSY color definitions). Changed all code so that html co...
gjocodonlib.pm  1.12  5 years  golsen  Some clean-up in anticipation of getting this into production.
gjocluster.pm  1.1  5 years  golsen  Some support for clustering and generating representatives of an alignment at an...
gjoavllib.pm  1.1  5 years  golsen  Some support for clustering and generating representatives of an alignment at an...
gjoalignment.pm  1.49  5 years  golsen  Some new routines.
gjoalignandtree.pm  1.20  7 years  golsen  Add more flexibility ot extract_with_psiblast. Fix most of the temporary file na...
gjoalign2html.pm  1.11  7 years  golsen  Support for residue color = none.
genome_frequencies.pm  1.3  7 years  golsen  Minor changes to GenomeCodonUsages.pm Add notice that genome_frequencies.pm will...
gd_tree_0.pm  1.5  9 years  golsen  Extensive reworking of color management.
find_special_proteins.pm  1.13  7 years  golsen  Change the temporary_directory function to be that in SeedAware.pm
find_homologs.pm  1.10  6 years  olson  Remove unused references to FIG_Config. add sas directive to find_homologs.
ffxtree.pm  1.30  5 years  fangfang  fix bug in raxml
fastDNAml.pm  1.2  14 years  olson  Added license words.
display_related_genomes.pm  1.2  9 years  golsen  Minor documentation changes in code.
crispr.pm  1.4  5 years  golsen  Fix bug in which $replen was overloaded, and not reinitialized.
compare_coding.pm  1.10  9 years  golsen  Integrate use of SeedAware.pm
collect_related_sequences.pm  1.6  9 years  golsen  Update to use SeedAware.pm (and do some general clean-up).
clustaltree.pm  1.3  10 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
bidir_best_hits.pm  1.1  8 years  golsen  Code for bidirectional best hits in a form used by codon usage analysis software...
align_and_tree_test.pm  1.1  8 years  golsen  Temp code for using DBMS version of alignment and tree access.
__init__.py  1.2  14 years  olson  Added license words.
WriteGenbank.pm  1.2  9 years  gdpusch  Forgot trailing "1;" :(
WriteEMBL.pm  1.1  8 years  gdpusch  Initial checkin --- probably still needs work.
WikiTools.pm  1.8  11 years  parrello  Fixed a glitch in list rendering.
WebColors.pm  1.16  9 years  paczian  re-added circle color scheme
UserData.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
UserDB.pm  1.2  14 years  olson  Added license words.
UpdateServer.pm  1.2  8 years  disz  Remove Sapling stuff`
UnvSubsys.pm  1.20  12 years  paczian  added missing "use HTML;"
TreeFC.pm  1.1  6 years  fangfang  Add module for tree-based functional coupling.
TransactionProcessor.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
Tracer.pm  1.137  5 years  olson  Don't change $FIG_Config::temp
Tpn_Int_Reps.pm  1.1  5 years  jdavis  *** empty log message ***
ToCall.pm  1.12  8 years  gdpusch  Modified to allow FIGfam IDs with arbitrarily many digits, and to fail safe if F...
TestUtils.pm  1.12  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
TableCell.pm  1.1  8 years  golsen  Support for a new sims table format.
TBLstuff.pm  1.2  11 years  overbeek  minor fixes
SubsystemPrimer2SS.pm  1.2  8 years  overbeek  update index
SubsystemPrimer.pm  1.8  8 years  overbeek  better help
Subsystem.pm  1.154  8 years  olson  forgot the delete on subsystem_nonaux_role
StrepRepeats.pm  1.2  6 years  olson  add raw-repeats method
Stats.pm  1.10  8 years  parrello  KBase changes and C-based YAML.
StandaloneSims.pm  1.1  11 years  olson  FIGM/FIGV changes for sims between RAST orgs.
SproutSearch.pm  1.11  14 years  olson  Added license words.
SproutFIG.pm  1.10  14 years  olson  Added license words.
SimsTable.pm  1.11  6 years  golsen  Work around an issue when a user-supplied blast query has a fig| id that is not ...
SimFC.pm  1.3  11 years  overbeek  handle deleted FIDs and failure to get translations
Sim2.pm  1.1  9 years  overbeek  tree sims
Sim.pm  1.17  7 years  golsen  Fix duplicate defintion of new(). Add usage().
Signatures.pm  1.2  9 years  parrello  Various POD fixes.
ServerThing.pm  1.90  7 years  olson  Add metabolic_reconstruction to the list of commands sent to the slow queue.
ServerScripts.pm  1.5  9 years  overbeek  add summarize_MG_output
ServSubsysRow.pm  1.11  8 years  overbeek  minor fixes
ServRole.pm  1.5  8 years  overbeek  fixes to make Sapling version work
ServReaction.pm  1.5  8 years  overbeek  fixes
ServOTU.pm  1.8  8 years  overbeek  minor fixes
ServIndex.pm  1.2  8 years  overbeek  starting to work
ServGenome.pm  1.15  8 years  overbeek  pass user
ServFeature.pm  1.24  8 years  overbeek  allow updates
ServFIGfam.pm  1.7  8 years  overbeek  minor changes
ServComplex.pm  1.6  8 years  overbeek  fixes to make Sapling version work
SeqStore.pm  1.1  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
SeedV.pm  1.10  8 years  olson  fix nasty boundary bug
SeedUtils.pm  1.72  5 years  golsen  Some code clean-up. Some additonal comments. Some speed-ups.
SeedSims.pm  1.1  11 years  overbeek  additions to support partitioning of sims
SeedSearch.pm  1.4  7 years  olson  add new type
SeedHTML.pm  1.3  10 years  olson  More distro fixes.
SeedEnv.pm  1.5  6 years  olson  Make conditional on existence of ModelSEED.
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
SeedCodonUsageToKBase.pm  1.1  7 years  golsen  Build files to support moving codon usage data into KBase.
SeedCodonUsage.pm  1.3  5 years  golsen  Increased functionality. Improved documentation.
SeedAware.pm  1.19  6 years  olson  fix system_with_redirect for use with fcgi
SeedAlignAndTreeToKBase.pm  1.7  7 years  fangfang  Remove the superseded_by column for both Alignment.tab and Tree.tab to match the...
ScriptThing.pm  1.8  9 years  parrello  Expression vector support methods.
Scenario.pm  1.10  9 years  dejongh  change scenario handling to use path_info.txt
SaplingGenomeData.pm  1.3  6 years  fangfang  fix bug in all_genome_peg_data()
SaplingCodonUsage.pm  1.2  5 years  golsen  Increased functionality. Improved documentation.
SaplingAlignmentPsiBLAST.pm  1.2  5 years  fangfang  move representative_alignment code to gjoalignment
SapCompareRegions.pm  1.6  5 years  olson  Use the local SEED's FIG::sims if possible to retrieve sims; this will enable re...
SampleDir.pm  1.4  9 years  olson  More analysis fixes; user-agent setting.
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
SUPserver.pm  1.1  9 years  parrello  New Sapling update support.
SUP.pm  1.3  8 years  parrello  Removed obsolete alignment stuff.
SSserver.pm  1.17  10 years  parrello  Removed from the SAS distribution.
SSU_rRNA_reps.pm  1.5  6 years  golsen  Add note indicating that this is now depricated. use RNA_rep_SSU_rRNA
SS.pm  1.13  10 years  parrello  More documentation cleanup.
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
SEEDServer.pm  1.3  7 years  olson  Add get_genome_features
SEEDImpl.pm  1.4  7 years  olson  Add get_genome_features
SEEDClient.pm  1.3  7 years  olson  Add get_genome_features
SEED.spec  1.3  7 years  olson  Add get_genome_features
SAPtutorial.pm  1.10  10 years  parrello  Fixed some errors in examples of ID types.
SAPserver.pm  1.14  9 years  parrello  Support for local SQLite servers.
SAP.pm  1.190  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
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.
RiboProtQC.pm  1.2  6 years  fangfang  fix bug in detecting genomes with duplicated ribo proteins
RemoteCustomAttributes.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
ReactionPath.pm  1.1  9 years  parrello  Added new method to compute reaction paths.
RNA_reps_SSU_rRNA.pm  1.5  6 years  olson  make sas components.
RNA_reps_LSU_rRNA.pm  1.5  6 years  olson  make sas components.
RNA_reps_5S_rRNA.pm  1.5  6 years  olson  make sas components.
README  16 years  efrank   import
RC.pm  1.33  7 years  disz  FIxed genome_data call
RASTserver.pm  1.25  7 years  redwards  Adding the ability to get users jobs
RAST_submission.pm  1.35  5 years  olson  Add new export types (pulled from last production version in /vol/rast-prod/FIGd...
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
Prot_reps_drug_resistance.pm  1.2  6 years  golsen  Fixed spelling of $max_exptrapolate to be $max_extrapolate. The value is exporte...
ProtSims.pm  1.20  8 years  gdpusch  Turn off the annoying and confusing "Blat returns 0" diagnostic message unless $...
ProtFamsLite.pm  1.2  11 years  arodri7  added functions and made functions work
ProtFams.pm  1.3  11 years  arodri7  added functions and made functions work
ProtFamLite.pm  1.2  11 years  arodri7  added functions and made functions work
Prodigal.pm  1.7  5 years  olson  Tmpdir fixes.
PinnedRegions.pm  1.40  6 years  olson  Add support for kmer-based pin detection.
PickFeatureSet.pm  1.2  11 years  overbeek  add .html to HTML files
Phage.pm  1.4  6 years  redwards  adding phage stuff
PersistentSets.pm  1.3  8 years  disz  filled in all functions
PartitionSeqs.pm  1.3  10 years  overbeek  return either scalar or list
ParalogResolution.pm  1.6  8 years  golsen  Add a fraction identity filter of finding paralogs.
PageBuilder.pm  1.15  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
PG.pm  1.8  6 years  overbeek  handle extraction of genome ids better
P2Pupdate.pm  1.64  8 years  olson  Fix indexing upon subsystem installation
P2P.pm  1.31  14 years  olson  Added license words.
Overlap.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
OddStarts_ref.pm  1.1  11 years  overbeek  add the ability to find TIF3
Observation.pm  1.83  9 years  redwards  correcting web links
NewGenome.pm  1.82  8 years  gdpusch  Fixed 0 == undef bug on contig IDs.
NRTools.pm  1.4  10 years  olson  update to new metadata standard
NCBI_taxonomy.pm  1.5  6 years  golsen  Fix code to match current return from NCBI.
NCBI_genetic_code.pm  1.4  8 years  golsen  Add start codons to genetic code data.
MinimalTracer.pm  1.1  9 years  olson  More FS_RAST modes & supporting code for SAS use.
MgRastSims.pm  1.1  10 years  redwards  a new package for getting sims for the mg-rast
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
MergeTransactions.pm  1.3  12 years  parrello  Changed POD format for better compatability with Wiki.
Markups.pm  1.2  12 years  parrello  Changed POD format for better compatability with Wiki.
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
Makefile  1.15  6 years  olson  Changes from pangenome work.
MSSeedSupport.pm  1.1  8 years  devoid  Adding MSSeedSupport, a SVR package for ModelSEED to support genomes from RAST.
MD5Computer.pm  1.5  6 years  parrello  Sapling fixes.
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
ListServerScripts.pm  1.2  9 years  parrello  Fixed to point to PUBSEED server for documentation.
LinksUI.pm  1.20  8 years  overbeek  try to pass user correctly
KmersOld.pm  1.1  10 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
Kmers2013.pm  1.1  7 years  disz  new kmer modules
Kmers.pm  1.40  5 years  olson  add neighbor computation code.
KmerMgr.pm  1.6  6 years  olson  add sas tag
KmerClient.pm  1.2  5 years  olson  Ensure the module still loads if genome map load fails.
KmerClassifier.pm  1.2  6 years  olson  add sas decl
KGMLData.pm  1.5  6 years  redwards  Removing the defined(%hash) is deprecated and defined(@array) is deprecated warn...
KGML.pm  1.4  12 years  olson  Hope college modifications.
KBaseCodonUsage.pm  1.2  5 years  golsen  Code clean up. Improved documentation. Some increased functionality.
KBRpcContext.pm  1.1  8 years  olson  KB context object for RPC support.
JobScheduler.pm  1.10  9 years  olson  Put. The Scheduler. Back.
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
IS_Subroutines.pm  1.2  5 years  jdavis  blastplus in blastinterface.pm has a bug so I turned off blastplus in %opts
IS_Data.pm  1.1  5 years  jdavis  *** empty log message ***
IDclient.pm  1.3  5 years  olson  Don't fail if we can't match a sequence.
HtmlPageParser.pm  1.2  14 years  olson  Added license words.
HTML.py  1.6  14 years  olson  Added license words.
HTML.pm  1.137  6 years  golsen  Add a <META html-equiv...> tag in <HEAD>
GenomeTypeObject.pm  1.19  5 years  olson  Add gc computation.
GenomeSetServer.pm  1.1  5 years  olson  New genome set stuff.
GenomeSetImpl.pm  1.1  5 years  olson  New genome set stuff.
GenomeSetClient.pm  1.1  5 years  olson  New genome set stuff.
GenomeSet.spec  1.1  5 years  olson  New genome set stuff.
GenomeSelector.pm  1.3  6 years  golsen  Fix the case of the directory with the JavaScript.
GenomeMetaDatabase.pm  1.1  10 years  jared  *** empty log message ***
GenomeMetaDB.pm  1.5  10 years  jared  added update_path
GenomeMeta.pm  1.16  10 years  olson  Add lock retries; probably not needed now that I think I've fixed FileLocking bu...
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
GenomeIDMap.pm  1.4  14 years  olson  Added license words.
GenomeCodonUsages.pm  1.3  7 years  golsen  Very minor changes.
GenoGraphics.pm  1.30  7 years  golsen  Minor changes due to redefinitions. Add "no warnings qw( redefine );"
GenerateClusters.pm  1.2  7 years  overbeek  require % iden >= 50 for projection: UNTESTED
FullLocation.pm  1.25  10 years  parrello  Added a method to compute the total location length.
FudgeTransactions.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
Find_RNAs.pm  1.5  6 years  olson  cleanup work directories
FileLocking.pm  1.4  9 years  olson  Changes for DesktopRast. CVHnS: ------------------------------------------------...
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FS_RAST.pm  1.39  7 years  overbeek  fix default of genetic code
FIGtree.pm  1.3  14 years  olson  Added license words.
FIGrpc.pm  1.3  14 years  olson  Added license words.
FIGnet.pm  1.2  14 years  olson  Added license words.
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
FIGgjo.pm  1.5  8 years  golsen  Support for better role coloring and formatting.
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
FIGV.pm  1.104  5 years  olson  Fix old little bug that completely broke FIGV::feature_location_bulk.
FIGUtilities.pm  1.2  14 years  olson  Added license words.
FIGStatisticalModels.pm  1.8  7 years  gdpusch  mean() modified to use round-off-protected Kahan summation. stdev() modified to ...
FIGRules.pm  1.56  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
FIGM.pm  1.22  5 years  olson  Rollup of RASTtk changes.
FIGGenDB.pm  1.6  14 years  olson  Added license words.
FIGAttributes.pm  1.4  11 years  overbeek  get rid of something
FIG2.py  1.2  14 years  olson  Added license words.
FIG.py  1.13  14 years  olson  Added license words.
FIG.pm  1.921  5 years  overbeek  minor bug in subsystems_info
FFserver.pm  1.23  10 years  parrello  Removed from the SAS distribution.
FFs.pm  1.58  5 years  olson  Tie the translation btree.
FFB3.pm  1.1  8 years  olson  figfam build helper module
FF.pm  1.36  6 years  olson  Add SAS declarations.
FC.pm  1.22  7 years  parrello  Fixed to improve performance of pairset deletions.
FBasicLocation.pm  1.1  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
FBAMODELserver.pm  1.5  8 years  chenry  Moving FBAMODELserver.pm to FigKernelPackages, and changing URL.
ExpressionDir.pm  1.12  8 years  olson  add compute_pearson_corr
ErrorMessage.pm  1.2  10 years  olson  remove unused use CGI.
DrugResistanceDB.pm  1.1  6 years  overbeek  drug resistance reps db
DocUtils.pm  1.18  10 years  parrello  Added documentation functions to the Sapling server.
Dlits.pm  1.6  6 years  olson  Catch bad pmids so db call doesn't crash.
Diagram.pm  1.22  6 years  seaver  Removing STDERR debug statements from Diagram.pm
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
DBKernel.pm  1.82  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
CrossSeedLinks.pm  1.1  6 years  golsen  Rudimentary support for links between SEEDs. Nothing currenly uses it, but it se...
Corresponds.pm  1.1  8 years  overbeek  finally debugged
CorrespondenceCache.pm  1.2  9 years  parrello  Added experiment filter to "fid_experiments". Fixed correspondence cache to work...
Correspondence.pm  1.4  9 years  overbeek  correct the identity check
CorrTableEntry.pm  1.5  8 years  overbeek  add 20th column - clear_bbhs
Contigs.pm  1.1  11 years  overbeek  new Contigs.pm and compare_coding.pm
ContigMD5.pm  1.3  12 years  olson  clone the digest so that checksum() may be called multiple times
Construct.pm  1.2  14 years  olson  Added license words.
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
CompareMR.pm  1.8  11 years  paczian  cutting comments off of functional roles
CommonCGI.pm  1.1  7 years  olson  common cgi code.
CodonUsageTable.pm  1.5  5 years  golsen  Inceased functionality. Removal of some unnecessary module names.
Cmd2HTML.pm  1.11  7 years  overbeek  add compound_to_reactions
Clustering.pm  1.6  9 years  overbeek  added double and triple linkage
ClusterWorker.pm  1.2  14 years  olson  Added license words.
Cluster.pm  1.11  14 years  olson  Added license words.
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
CloseStrains.pm  1.19  5 years  overbeek  counts in table headers
CloseGenomes.pm  1.2  7 years  olson  add sas tag
ClientThing.pm  1.32  5 years  parrello  Added support for Core Sapling server.
Clearinghouse.py  1.12  8 years  olson  Use new SS clearinghouse on pubseed.
Clearinghouse.pm  1.7  5 years  olson  Don't spit output to stdout.
Classes.pm  1.1  14 years  mkubal  added Organism class
ChromosomalClusters.pm  1.11  8 years  parrello  Added "roles_to_proteins" method.
CallByProjection.pm  1.4  7 years  overbeek  ross fixes
COserver.pm  1.13  10 years  parrello  Removed from the SAS distribution.
COPYING.TXT  1.1  14 years  olson  add license file
CO.pm  1.6  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
CGIAlignTreeViewer.pm  1.24  7 years  golsen  Convert image files to use new temporary file name functions.
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
Boolean.pm  1.3  6 years  overbeek  handle debug str better
BlastInterface.pm  1.22  5 years  golsen  Another HSP filter option (normalized bit score). Some potential speed-up in fil...
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
BlankSVP.pm  1.1  8 years  olson  Script & infrastructure for creating easy seedviewer pages.
Biochemistry.pm  1.2  5 years  overbeek  update reaction stuff
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
BerkTable.pm  1.2  9 years  olson  fix arg
BasicLocation.pm  1.24  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
BadCall.pm  1.4  12 years  parrello  Replaced obsolete AddToListMap method.
BBasicLocation.pm  1.1  5 years  parrello  CDMI and Sprout load fixes. Locations fixes.
Assignments.pm  1.17  11 years  overbeek  remove impact of our annotations on making assignments using auto_assign
ApplyTransactions.pm  1.7  12 years  parrello  Changed POD format for better compatability with Wiki.
Annotation.pm  1.4  12 years  parrello  Added a TITLE statement for the Wiki.
AnnoClearinghouse.pm  1.44  11 years  wilke  Modified sql query to ? syntax
AlignsAndTreesServer.pm  1.29  5 years  golsen  Fix bug in variable declaration.
AlignsAndTrees.pm  1.17  7 years  fangfang  add server side implementation of alignments_metadata_by_md5() and alignment...
AlignTree.pm  1.51  5 years  fangfang  add CoreSEED db
AliasAnalysis.pm  1.13  7 years  parrello  Added IMG and ERIC.
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
AliTreeSims.pm  1.8  8 years  fangfang  fixed a variable name
AliTreeIdConvert.pm  1.1  9 years  golsen  Functions for interconverting MD5 and peg ids of alignments and trees in the SEE...
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
ATserver.pm  1.2  9 years  fangfang  default url set to biobig
AT.pm  1.6  9 years  fangfang  add blast function
ANNOserver.pm  1.26  7 years  olson  Add support for passing -detailed through to dna kmers. Add support for retrievi...
ANNO.pm  1.13  7 years  olson  Finish support for detailed kmers in dna.
ALITREserver.pm  1.1  9 years  parrello  New alignment/tree server stuff.
ALITRE.pm  1.6  7 years  fangfang  add server side implementation of alignments_metadata_by_md5() and alignment...
ACHserver.pm  1.16  10 years  parrello  Removed from the SAS distribution.
ACH.pm  1.7  10 years  disz  changed doc to say XXserver->new() insetad of XX->new

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