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Index of /FigKernelPackages

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File (rev) Rev. Age Author Last log entry
 Parent Directory        
tree_utilities.pm  1.20  10 years  olson  Add more modules to the SAS toolkit.
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  1.5  10 years  golsen  Add some reference sequences and replace ; with @ in functions.
representative_sequences.pm  1.18  9 years  golsen  Huge restructuring of the rep_seq() and rep_seq2() functions. Better performanc...
raelib.pm  1.45  9 years  redwards  adding a pegs in order method (should probably be in FIG.pm cos way useful)
raedraw.pm  1.14  12 years  parrello  Changed POD heading levels.
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
protdist_neighbor.pm  1.1  13 years  golsen  A package for protdist and neighbor PHYLIP trees.
proml.pm  1.9  10 years  golsen  Minor updates to SEED awareness.
model.pm  1.36  9 years  dejongh  change scenario handling to use path_info.txt
gjostat.pm  1.3  9 years  golsen  Convert die to confess.
gjoseqlib.pm  1.25  9 years  golsen  Just some additions to the function descriptions.
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  1.8  9 years  golsen  Fix two minor typographical errors in the documentation.
gjonewicklib.pm  1.25  9 years  golsen  Change behavior of reroot_tree() to ignore distance if there is only one node.
gjonativecodonlib.pm  1.2  9 years  golsen  Forgot the SAS component lines.
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
gjolib.pm  1.3  10 years  olson  Add more modules to the SAS toolkit.
gjogff.pm  1.2  9 years  golsen  Changes to fix some bugs in GenBank format reading and writing. Changes to deal ...
gjogenbank.pm  1.9  9 years  golsen  Some sites do not include a blank space after "ORIGIN".
gjocolorlib.pm  1.7  9 years  golsen  Added support for luma (HSY color definitions). Changed all code so that html co...
gjocodonlib.pm  1.2  9 years  golsen  Forgot the SAS component lines.
gjoalignment.pm  1.38  9 years  fangfang  update align_with_mafft
gjoalignandtree.pm  1.16  9 years  golsen  Minor consistency improvements in options, and remove redundancy in getting the ...
gjoalign2html.pm  1.5  9 years  fangfang  SAS component
gd_tree_0.pm  1.5  10 years  golsen  Extensive reworking of color management.
find_special_proteins.pm  1.12  9 years  olson  typod the declaration
find_homologs.pm  1.4  9 years  golsen  use SeedAware Many changes in details of code.
ffxtree.pm  1.23  9 years  fangfang  replace newick_subtree with rooted_newick_subtree
fastDNAml.pm  1.2  14 years  olson  Added license words.
display_related_genomes.pm  1.2  9 years  golsen  Minor documentation changes in code.
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  11 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
__init__.py  1.2  14 years  olson  Added license words.
WriteGenbank.pm  1.2  9 years  gdpusch  Forgot trailing "1;" :(
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.
UnvSubsys.pm  1.20  12 years  paczian  added missing "use HTML;"
TransactionProcessor.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
Tracer.pm  1.132  9 years  parrello  Added an option to display configuration data to the command-line setup utility....
ToCall.pm  1.11  11 years  gdpusch  Major rewrite to prevent already-found PEGs from being re-called by every stage ...
TestUtils.pm  1.11  10 years  parrello  Fixed display glitch for pure white space.
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
TBLstuff.pm  1.2  11 years  overbeek  minor fixes
Subsystem.pm  1.149  9 years  olson  Subsystem speedup fixes.
Stats.pm  1.8  11 years  parrello  Added a method to extract saved messages.
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.
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  1.14  10 years  olson  Distro fixups
Signatures.pm  1.2  9 years  parrello  Various POD fixes.
ServerThing.pm  1.73  9 years  parrello  New method for features expressed in a given fraction of the experiments.
ServerScripts.pm  1.5  10 years  overbeek  add summarize_MG_output
SeedV.pm  1.9  9 years  gdpusch  Changed a debugging line to print to STDERR, not STDOUT; print only if VERBOSE.
SeedUtils.pm  1.60  9 years  parrello  Adjustments to loader utilities.
SeedSims.pm  1.1  11 years  overbeek  additions to support partitioning of sims
SeedHTML.pm  1.3  10 years  olson  More distro fixes.
SeedEnv.pm  1.4  9 years  olson  Use new path to FBAModelSerer
SeedDas.pm  1.22  13 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
SeedAware.pm  1.7  9 years  olson  add win32 support to executable_For
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
SapCompareRegions.pm  1.3  9 years  olson  Change to output format; outer hash with fid => results, rows are now hashes wit...
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  1.2  9 years  parrello  New methods for alignment data.
SSserver.pm  1.17  10 years  parrello  Removed from the SAS distribution.
SSU_rRNA_reps.pm  1.3  9 years  golsen  Adjust end of one reference sequence by padding it slightly.
SS.pm  1.13  10 years  parrello  More documentation cleanup.
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
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  1.155  9 years  parrello  New method for features expressed in a given fraction of the experiments.
RemoteCustomAttributes.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
README  16 years  efrank   import
RC.pm  1.2  14 years  olson  Added license words.
RASTserver.pm  1.23  9 years  gdpusch  Fixed bugs in and added more support for Viral and Euk jobs.
RAST_submission.pm  1.28  9 years  olson  typofix
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
ProtSims.pm  1.19  9 years  overbeek  turn off debugging print
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
PinnedRegions.pm  1.34  9 years  olson  fix unlink here too
PickFeatureSet.pm  1.2  11 years  overbeek  add .html to HTML files
Phage.pm  1.3  9 years  redwards  minor correction
PartitionSeqs.pm  1.3  11 years  overbeek  return either scalar or list
ParalogResolution.pm  1.5  11 years  golsen  Modifications to support line-drawing character set in tree printer plots.
PageBuilder.pm  1.14  12 years  parrello  Changed POD format for better compatability with Wiki.
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
P2Pupdate.pm  1.62  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
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  1.80  10 years  parrello  Protected a "new FIG" in open code with an eval. THIS MUST BE FIXED.
NRTools.pm  1.4  11 years  olson  update to new metadata standard
NCBI_taxonomy.pm  1.4  9 years  golsen  Add more formats in which abbreviated lineages can be returned. Add long form of...
NCBI_genetic_code.pm  1.3  9 years  olson  add SAS header
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  1.13  9 years  gdpusch  Initial checkin of module to facilitate writeing GenBank output.
LogReader.pm  1.1  12 years  parrello  Added to facilitate reading the error log.
ListServerScripts.pm  1.2  9 years  parrello  Fixed to point to PUBSEED server for documentation.
KmersOld.pm  1.1  10 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
Kmers.pm  1.28  9 years  olson  fix off-by-one
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
KGML.pm  1.4  13 years  olson  Hope college modifications.
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
HtmlPageParser.pm  1.2  14 years  olson  Added license words.
HTML.py  1.6  14 years  olson  Added license words.
HTML.pm  1.130  11 years  arodri7  added links to set_prot_links
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.
GenoGraphics.pm  1.24  10 years  golsen  Back pedal on the attempt to diagnose jpeg and png availability in GenoGraphics
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.
FileLocking.pm  1.4  9 years  olson  Changes for DesktopRast. CVHnS: ------------------------------------------------...
FigGFF.pm  1.22  13 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FS_RAST.pm  1.35  9 years  overbeek  minor updates
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  1.3  13 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
FIG_CGI.pm  1.11  12 years  olson  Add annotation support to FIGV. Add FIGM.
FIGV.pm  1.97  9 years  olson  Fix the long-standing bug where all_contigs returned the number of contigs with ...
FIGUtilities.pm  1.2  14 years  olson  Added license words.
FIGStatisticalModels.pm  1.7  9 years  gdpusch  Initial checkin of module to facilitate writeing GenBank output.
FIGRules.pm  1.54  10 years  olson  Optimize to_structured_english.
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
FIGM.pm  1.18  9 years  olson  Add FIGV and FIGM function_of_bulk
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  1.838  9 years  olson  add features_in_atomic_regulon
FFserver.pm  1.23  10 years  parrello  Removed from the SAS distribution.
FFs.pm  1.49  9 years  olson  Clean up errors.
FF.pm  1.35  9 years  disz  FigFam 6 digit fix
FC.pm  1.21  10 years  parrello  Fixed a bug in "co_occurrence_evidence".
ExpressionDir.pm  1.10  9 years  olson  Support for duplicate match removal. Support for using Subsystems/{bindings,subs...
ErrorMessage.pm  1.2  10 years  olson  remove unused use CGI.
DocUtils.pm  1.18  10 years  parrello  Added documentation functions to the Sapling server.
Diagram.pm  1.19  9 years  redwards  fixing jpeg images
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
DBKernel.pm  1.65  9 years  olson  Caching / FCGI speedup modifications.
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  1.4  9 years  olson  Add num_matching_functions for column 19
Contigs.pm  1.1  11 years  overbeek  new Contigs.pm and compare_coding.pm
ContigMD5.pm  1.3  13 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
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
ClientThing.pm  1.23  9 years  olson  alternate fix :-) pull the initialization of the list to the constructor, ensure...
Clearinghouse.py  1.11  11 years  olson  Fix now-broken MCS URLs.
Clearinghouse.pm  1.5  11 years  olson  fix clearinghouse urls.
Classes.pm  1.1  14 years  mkubal  added Organism class
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
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
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
BinarySearch.pm  1.1  13 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  1.19  10 years  parrello  Updated to Sapling Server for Berkeley.
BadCall.pm  1.4  12 years  parrello  Replaced obsolete AddToListMap method.
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  1.3  9 years  overbeek  debugged
AlignsAndTrees.pm  1.4  9 years  overbeek  debugged
AlignTree.pm  1.37  9 years  fangfang  update
AliasAnalysis.pm  1.11  9 years  parrello  Updates for single-genome loader.
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
AliTreeSims.pm  1.6  9 years  fangfang  remove old code
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  1.20  9 years  parrello  Fixed a POD error.
ANNO.pm  1.9  9 years  parrello  Fixed missing method problem.
ALITREserver.pm  1.1  9 years  parrello  New alignment/tree server stuff.
ALITRE.pm  1.1  9 years  parrello  New alignment/tree server stuff.
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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