[Bio] / FigKernelPackages Repository:
ViewVC logotype

Index of /FigKernelPackages

Files shown:335 (Show 32 dead files)
Sticky Tag:


File Rev. Age Author Last log entry
 Parent Directory        
Export/        
tests/        
ACH.pm  1.7  7 years  disz  changed doc to say XXserver->new() insetad of XX->new
ACHserver.pm  1.16  7 years  parrello  Removed from the SAS distribution.
ALITRE.pm  1.6  5 years  fangfang  add server side implementation of alignments_metadata_by_md5() and alignment...
ALITREserver.pm  1.1  6 years  parrello  New alignment/tree server stuff.
ANNO.pm  1.14  21 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
ANNOserver.pm  1.27  21 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
AT.pm  1.6  6 years  fangfang  add blast function
ATserver.pm  1.2  6 years  fangfang  default url set to biobig
AdaboostClassifierAMRv1.pm  1.1  20 months  olson  Jim Davis' classifier code.
AdaboostClassify.pm  1.4  9 months  olson  Move to Nov_2016_AMR_Classifiers classifier module. Adds required changes to bla...
AliTree.pm  1.5  10 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
AliTreeIdConvert.pm  1.1  6 years  golsen  Functions for interconverting MD5 and peg ids of alignments and trees in the SEE...
AliTreeSims.pm  1.8  5 years  fangfang  fixed a variable name
AliTrees.pm  1.4  10 years  overbeek  fix AliTrees.pm to fail gracefully
AliasAnalysis.pm  1.13  5 years  parrello  Added IMG and ERIC.
AlignTree.pm  1.53  22 months  fangfang  remove empty sequences in trimmed alignments
AlignsAndTrees.pm  1.17  5 years  fangfang  add server side implementation of alignments_metadata_by_md5() and alignment...
AlignsAndTreesServer.pm  1.29  3 years  golsen  Fix bug in variable declaration.
AminoAcidMatrix.pm  1.1  2 months  golsen  Tools for handling amino acid scoring matrices. Has many matrices built-in. Prov...
AnnoClearinghouse.pm  1.44  8 years  wilke  Modified sql query to ? syntax
Annotation.pm  1.4  9 years  parrello  Added a TITLE statement for the Wiki.
ApplyTransactions.pm  1.7  9 years  parrello  Changed POD format for better compatability with Wiki.
Assignments.pm  1.17  9 years  overbeek  remove impact of our annotations on making assignments using auto_assign
BBasicLocation.pm  1.2  2 years  parrello  Changes copied from SEEDtk project.
BadCall.pm  1.4  9 years  parrello  Replaced obsolete AddToListMap method.
BasicLocation.pm  1.29  3 months  parrello  Changes copied from SEEDtk project.
BerkTable.pm  1.2  7 years  olson  fix arg
BinarySearch.pm  1.1  10 years  overbeek  just add a binary search so I do not have to recode it again
Biochemistry.pm  1.4  2 years  overbeek  fixes for reactions
BlankSVP.pm  1.1  5 years  olson  Script & infrastructure for creating easy seedviewer pages.
Blast.pm  1.5  9 years  overbeek  close TMP files in Blast.pm
BlastInterface.pm  1.28  2 months  golsen  Added access functions for HSP information. Added much more support for PSSMs an...
Boolean.pm  1.4  7 months  overbeek  fix tree_utilities parser
ButtonArray.pm  1.1  9 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
CGIAlignTreeViewer.pm  1.24  4 years  golsen  Convert image files to use new temporary file name functions.
CO.pm  1.6  7 years  disz  changed doc to say XXserver->new() insetad of XX->new
COPYING.TXT  1.1  11 years  olson  add license file
COserver.pm  1.13  7 years  parrello  Removed from the SAS distribution.
CallByProjection.pm  1.5  4 months  olson  Remove hopefully unused dependencies.
ChromosomalClusters.pm  1.11  6 years  parrello  Added "roles_to_proteins" method.
Classes.pm  1.1  11 years  mkubal  added Organism class
Clearinghouse.pm  1.7  3 years  olson  Don't spit output to stdout.
Clearinghouse.py  1.12  5 years  olson  Use new SS clearinghouse on pubseed.
ClientThing.pm  1.32  3 years  parrello  Added support for Core Sapling server.
CloseGenomes.pm  1.2  5 years  olson  add sas tag
CloseStrains.pm  1.30  2 years  overbeek  fix temp for sorts
ClosestGenomes.pm  1.2  10 years  overbeek  fix AliTrees.pm to fail gracefully
Cluster.pm  1.11  11 years  olson  Added license words.
ClusterPairs.pm  1.1  19 months  parrello  Changes copied from SEEDtk project.
ClusterWorker.pm  1.2  11 years  olson  Added license words.
Clustering.pm  1.6  6 years  overbeek  added double and triple linkage
Cmd2HTML.pm  1.11  4 years  overbeek  add compound_to_reactions
CodonUsageTable.pm  1.6  2 years  golsen  Add ability to dynamically change links to alternative SEEDs. Other minor clean-...
CommonCGI.pm  1.1  4 years  olson  common cgi code.
CompareMR.pm  1.8  8 years  paczian  cutting comments off of functional roles
ComparedRegions.pm  1.6  10 years  parrello  Updated to improve performance.
ConservedDomainSearch.pm  1.4  2 years  olson  Bulk lookups. More feature generation fixes.
Construct.pm  1.2  11 years  olson  Added license words.
ContigMD5.pm  1.3  10 years  olson  clone the digest so that checksum() may be called multiple times
Contigs.pm  1.6  16 months  parrello  Changes copied from SEEDtk project.
CorrTableEntry.pm  1.5  6 years  overbeek  add 20th column - clear_bbhs
Correspondence.pm  1.4  6 years  overbeek  correct the identity check
CorrespondenceCache.pm  1.2  6 years  parrello  Added experiment filter to "fid_experiments". Fixed correspondence cache to work...
Corresponds.pm  1.1  5 years  overbeek  finally debugged
CrossSeedLinks.pm  1.1  3 years  golsen  Rudimentary support for links between SEEDs. Nothing currenly uses it, but it se...
DBKernel.pm  1.83  2 years  parrello  Added support for IGNORE and REPLACE in load_table.
DBrtns.pm  1.27  11 years  overbeek  Fix extra-args option to go at teh start of the list.
Diagram.pm  1.22  3 years  seaver  Removing STDERR debug statements from Diagram.pm
Dlits.pm  1.6  4 years  olson  Catch bad pmids so db call doesn't crash.
DocUtils.pm  1.18  8 years  parrello  Added documentation functions to the Sapling server.
DrugResistanceDB.pm  1.1  3 years  overbeek  drug resistance reps db
ErrorMessage.pm  1.2  7 years  olson  remove unused use CGI.
ExpressionDir.pm  1.12  5 years  olson  add compute_pearson_corr
FBAMODELserver.pm  1.5  6 years  chenry  Moving FBAMODELserver.pm to FigKernelPackages, and changing URL.
FBasicLocation.pm  1.2  2 years  parrello  Changes copied from SEEDtk project.
FC.pm  1.22  4 years  parrello  Fixed to improve performance of pairset deletions.
FF.pm  1.36  4 years  olson  Add SAS declarations.
FFB3.pm  1.1  5 years  olson  figfam build helper module
FFs.pm  1.58  3 years  olson  Tie the translation btree.
FFserver.pm  1.23  7 years  parrello  Removed from the SAS distribution.
FIG.pm  1.927  14 months  olson  Strike ModelSEED updates.
FIG.py  1.13  11 years  olson  Added license words.
FIG2.py  1.2  11 years  olson  Added license words.
FIGAttributes.pm  1.4  8 years  overbeek  get rid of something
FIGGenDB.pm  1.6  11 years  olson  Added license words.
FIGM.pm  1.22  3 years  olson  Rollup of RASTtk changes.
FIGO.pm  1.34  9 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
FIGRules.pm  1.56  6 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
FIGStatisticalModels.pm  1.8  4 years  gdpusch  mean() modified to use round-off-protected Kahan summation. stdev() modified to ...
FIGUtilities.pm  1.2  11 years  olson  Added license words.
FIGV.pm  1.105  21 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
FIG_CGI.pm  1.11  9 years  olson  Add annotation support to FIGV. Add FIGM.
FIGgjo.pm  1.5  5 years  golsen  Support for better role coloring and formatting.
FIGjs.pm  1.15  9 years  parrello  Fixed URL references.
FIGnet.pm  1.2  11 years  olson  Added license words.
FIGrpc.pm  1.3  11 years  olson  Added license words.
FIGtree.pm  1.3  11 years  olson  Added license words.
FQUtils.pm  1.1  5 months  parrello  Changes copied from SEEDtk project.
FS_RAST.pm  1.39  5 years  overbeek  fix default of genetic code
FastA.pm  1.1  4 months  parrello  Changes copied from SEEDtk project.
FastQ.pm  1.2  4 months  parrello  Changes copied from SEEDtk project.
FigGFF.pm  1.22  10 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FileLocking.pm  1.4  7 years  olson  Changes for DesktopRast. CVHnS: ------------------------------------------------...
Find_RNAs.pm  1.6  2 years  olson  Fix shell escape bug.
FudgeTransactions.pm  1.4  9 years  parrello  Changed POD format for better compatability with Wiki.
FullLocation.pm  1.25  7 years  parrello  Added a method to compute the total location length.
GenBankToGTO.pm  1.4  20 months  olson  Choose a contig identifier from VERSION, ACCESSION, LOCUS such that the contig i...
GenerateClusters.pm  1.2  4 years  overbeek  require % iden >= 50 for projection: UNTESTED
GenoGraphics.pm  1.30  4 years  golsen  Minor changes due to redefinitions. Add "no warnings qw( redefine );"
GenomeCodonUsages.pm  1.3  4 years  golsen  Very minor changes.
GenomeIDMap.pm  1.4  11 years  olson  Added license words.
GenomeLists.pm  1.2  9 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
GenomeMeta.pm  1.19  2 years  olson  Add missing module.
GenomeMetaDB.pm  1.5  8 years  jared  added update_path
GenomeMetaDatabase.pm  1.1  8 years  jared  *** empty log message ***
GenomeSelector.pm  1.3  3 years  golsen  Fix the case of the directory with the JavaScript.
GenomeSet.spec  1.1  3 years  olson  New genome set stuff.
GenomeSetClient.pm  1.1  3 years  olson  New genome set stuff.
GenomeSetImpl.pm  1.1  3 years  olson  New genome set stuff.
GenomeSetServer.pm  1.1  3 years  olson  New genome set stuff.
GenomeTypeObject.pm  1.43  5 months  parrello  Changes copied from SEEDtk project.
HTML.pm  1.137  4 years  golsen  Add a <META html-equiv...> tag in <HEAD>
HTML.py  1.6  11 years  olson  Added license words.
Hsp.pm  1.2  22 months  parrello  Changes copied from SEEDtk project.
HtmlPageParser.pm  1.2  11 years  olson  Added license words.
IDclient.pm  1.6  23 months  parrello  Changes copied from SEEDtk project.
IS_Data.pm  1.2  3 years  olson  Fixes for IS.
IS_Subroutines.pm  1.3  3 years  olson  Fixes for IS.
InsertIntoTree.pm  1.15  10 years  overbeek  check figfams fixes
InterfaceRoutines.pm  1.12  11 years  olson  readonly fixes; seed-run-job update to run from input file
JobScheduler.pm  1.10  6 years  olson  Put. The Scheduler. Back.
KBInvoke.pm  1.1  17 months  olson  Simple KBase-style RPC invocation module. Includes PATRIC/RAST/KBase login funct...
KBRpcContext.pm  1.1  5 years  olson  KB context object for RPC support.
KBaseCodonUsage.pm  1.2  3 years  golsen  Code clean up. Improved documentation. Some increased functionality.
KGML.pm  1.4  10 years  olson  Hope college modifications.
KGMLData.pm  1.5  4 years  redwards  Removing the defined(%hash) is deprecated and defined(@array) is deprecated warn...
KmerClassifier.pm  1.2  3 years  olson  add sas decl
KmerClient.pm  1.2  3 years  olson  Ensure the module still loads if genome map load fails.
KmerDb.pm  1.7  5 weeks  parrello  Changes copied from SEEDtk project.
KmerGutsNet.pm  1.2  22 months  olson  add sas
KmerMgr.pm  1.6  4 years  olson  add sas tag
KmerRepGenomes.pm  1.4  22 months  parrello  Changes copied from SEEDtk project.
Kmers.pm  1.42  16 months  olson  Remove duplicated FIG object creation.
Kmers2013.pm  1.1  4 years  disz  new kmer modules
KmersOld.pm  1.1  7 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
LinksUI.pm  1.20  5 years  overbeek  try to pass user correctly
ListServerScripts.pm  1.2  6 years  parrello  Fixed to point to PUBSEED server for documentation.
LogReader.pm  1.1  9 years  parrello  Added to facilitate reading the error log.
MD5Computer.pm  1.8  2 years  parrello  Fixed an error in ProcessContig.
MSSeedSupport.pm  1.1  5 years  devoid  Adding MSSeedSupport, a SVR package for ModelSEED to support genomes from RAST.
Makefile  1.15  4 years  olson  Changes from pangenome work.
MapIDs.pm  1.1  10 years  wilke  Initial version of functions to map different ids
MapToRef.pm  1.2  2 years  parrello  Changes copied from SEEDtk project.
Markups.pm  1.2  9 years  parrello  Changed POD format for better compatability with Wiki.
MergeTransactions.pm  1.3  9 years  parrello  Changed POD format for better compatability with Wiki.
MetaSubsystem.pm  1.4  9 years  bartels  added functions for genome manipulation
MgRastSims.pm  1.1  8 years  redwards  a new package for getting sims for the mg-rast
MinimalTracer.pm  1.1  7 years  olson  More FS_RAST modes & supporting code for SAS use.
MissingRoles.pm  1.1  20 months  parrello  Changes copied from SEEDtk project.
NCBI_genetic_code.pm  1.6  2 months  golsen  Added code "0", which is the universal code with the 3 common bacterial and arch...
NCBI_sequence.pm  1.2  2 months  golsen  Fix the URL to be https Add flexibility to format of a list of ids.
NCBI_taxonomy.pm  1.6  2 months  golsen  Changed to https.
NRTools.pm  1.4  8 years  olson  update to new metadata standard
NewGenome.pm  1.82  5 years  gdpusch  Fixed 0 == undef bug on contig IDs.
Nov_2016_AMR_Classifiers.pm  1.2  5 months  jdavis  Added Klebsiella classifiers
Observation.pm  1.84  2 years  redwards  removing defined @ which is deprecated and throws an error
OddStarts_ref.pm  1.1  8 years  overbeek  add the ability to find TIF3
Overlap.pm  1.4  9 years  parrello  Changed POD format for better compatability with Wiki.
P2P.pm  1.31  11 years  olson  Added license words.
P2Pupdate.pm  1.64  6 years  olson  Fix indexing upon subsystem installation
P3DataAPI.pm  1.25  12 days  olson  Add metadata to the query_cb callback. Also use the return value of query_cb to ...
P3Signatures.pm  1.7  2 months  parrello  Changes copied from SEEDtk project.
P3Utils.pm  1.14  5 weeks  parrello  Changes copied from SEEDtk project.
P3WorkspaceClient.pm  1.6  3 months  parrello  Changes copied from SEEDtk project.
PG.pm  1.8  4 years  overbeek  handle extraction of genome ids better
PHOB.pm  1.15  8 years  overbeek  switch from clustalw to muscle
PageBuilder.pm  1.15  6 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
ParalogResolution.pm  1.6  6 years  golsen  Add a fraction identity filter of finding paralogs.
ParseSIBEnzyme.pm  1.1  2 years  redwards  module and scripts to compare EC numbers to what we have in the SEED
PartitionSeqs.pm  1.3  8 years  overbeek  return either scalar or list
PersistentSets.pm  1.3  6 years  disz  filled in all functions
Phage.pm  1.4  4 years  redwards  adding phage stuff
PickFeatureSet.pm  1.2  8 years  overbeek  add .html to HTML files
PinnedRegions.pm  1.42  15 months  olson  Add more pattyfam support.
Prodigal.pm  1.8  21 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
PropagateGBMetadata.pm  1.3  19 months  olson  Adjust interval tree endpoint.
ProtFamLite.pm  1.2  8 years  arodri7  added functions and made functions work
ProtFams.pm  1.3  8 years  arodri7  added functions and made functions work
ProtFamsLite.pm  1.2  8 years  arodri7  added functions and made functions work
ProtSims.pm  1.20  6 years  gdpusch  Turn off the annoying and confusing "Blat returns 0" diagnostic message unless $...
Prot_reps_drug_resistance.pm  1.2  3 years  golsen  Fixed spelling of $max_exptrapolate to be $max_extrapolate. The value is exporte...
Quality.pm  1.6  9 years  parrello  Changed POD format for better compatability with Wiki.
RAST_submission.pm  1.37  16 months  olson  Add rasttk submission support
RASTlib.pm  1.8  3 months  parrello  Changes copied from SEEDtk project.
RASTserver.pm  1.26  2 years  olson  Add proxy support.
RC.pm  1.33  5 years  disz  FIxed genome_data call
README  1.1.1.1  13 years  efrank   import
RNA_reps_5S_rRNA.pm  1.5  3 years  olson  make sas components.
RNA_reps_LSU_rRNA.pm  1.5  3 years  olson  make sas components.
RNA_reps_SSU_rRNA.pm  1.5  3 years  olson  make sas components.
ReactionPath.pm  1.1  6 years  parrello  Added new method to compute reaction paths.
RemoteCustomAttributes.pm  1.8  9 years  parrello  Changed POD format for better compatability with Wiki.
RiboProtQC.pm  1.2  3 years  fangfang  fix bug in detecting genomes with duplicated ribo proteins
RoleParse.pm  1.1  5 months  parrello  Changes copied from SEEDtk project.
RoleRule.pm  1.1  6 years  parrello  New modules for analyzing protein family functions.
RoleRuleSubstring.pm  1.1  6 years  parrello  New modules for analyzing protein family functions.
SAP.pm  1.190  3 years  parrello  CDMI and Sprout load fixes. Locations fixes.
SAPserver.pm  1.14  6 years  parrello  Support for local SQLite servers.
SAPtutorial.pm  1.10  7 years  parrello  Fixed some errors in examples of ID types.
SEED.spec  1.4  23 months  olson  Add get_genomes() to the SEED RPC API.
SEEDClient.pm  1.5  23 months  olson  Add get_genomes() to the SEED RPC API.
SEEDImpl.pm  1.5  23 months  olson  Add get_genomes() to the SEED RPC API.
SEEDServer.pm  1.4  23 months  olson  Add get_genomes() to the SEED RPC API.
SFXlate.pm  1.119  8 years  parrello  Added "families_containing_peg".
SS.pm  1.13  7 years  parrello  More documentation cleanup.
SSU_rRNA_reps.pm  1.5  4 years  golsen  Add note indicating that this is now depricated. use RNA_rep_SSU_rRNA
SSserver.pm  1.17  7 years  parrello  Removed from the SAS distribution.
SUP.pm  1.3  5 years  parrello  Removed obsolete alignment stuff.
SUPserver.pm  1.1  6 years  parrello  New Sapling update support.
SameFunc.pm  1.17  9 years  overbeek  fix to SameFunc.pm
SampleDir.pm  1.4  6 years  olson  More analysis fixes; user-agent setting.
SapCompareRegions.pm  1.6  3 years  olson  Use the local SEED's FIG::sims if possible to retrieve sims; this will enable re...
SaplingAlignmentPsiBLAST.pm  1.3  2 years  golsen  Start adding support for extracting specific sequence positions based upon the a...
SaplingCodonUsage.pm  1.2  3 years  golsen  Increased functionality. Improved documentation.
SaplingGenomeData.pm  1.3  4 years  fangfang  fix bug in all_genome_peg_data()
Scenario.pm  1.10  6 years  dejongh  change scenario handling to use path_info.txt
ScriptThing.pm  1.9  2 years  parrello  Changes copied from SEEDtk project.
ScriptUtils.pm  1.6  5 months  parrello  Changes copied from SEEDtk project.
SeedAlignAndTreeToKBase.pm  1.7  5 years  fangfang  Remove the superseded_by column for both Alignment.tab and Tree.tab to match the...
SeedAware.pm  1.19  3 years  olson  fix system_with_redirect for use with fcgi
SeedCodonUsage.pm  1.4  2 years  golsen  Fix typo in the documentation.
SeedCodonUsageToKBase.pm  1.1  5 years  golsen  Build files to support moving codon usage data into KBase.
SeedDas.pm  1.23  2 months  olson  fix deprecated regular expression syntax
SeedEnv.pm  1.5  3 years  olson  Make conditional on existence of ModelSEED.
SeedHTML.pm  1.3  7 years  olson  More distro fixes.
SeedSearch.pm  1.7  3 months  olson  add crispr_array to indexed types list
SeedSims.pm  1.1  8 years  overbeek  additions to support partitioning of sims
SeedURLs.pm  1.2  2 years  parrello  Fixed spacing.
SeedUtils.pm  1.86  4 months  parrello  Changes copied from SEEDtk project.
SeedV.pm  1.11  21 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
SeqStore.pm  1.1  3 years  parrello  CDMI and Sprout load fixes. Locations fixes.
ServComplex.pm  1.6  5 years  overbeek  fixes to make Sapling version work
ServFIGfam.pm  1.7  5 years  overbeek  minor changes
ServFeature.pm  1.24  5 years  overbeek  allow updates
ServGenome.pm  1.15  5 years  overbeek  pass user
ServIndex.pm  1.2  5 years  overbeek  starting to work
ServOTU.pm  1.8  5 years  overbeek  minor fixes
ServReaction.pm  1.5  5 years  overbeek  fixes
ServRole.pm  1.5  5 years  overbeek  fixes to make Sapling version work
ServSubsysRow.pm  1.11  5 years  overbeek  minor fixes
ServerScripts.pm  1.5  7 years  overbeek  add summarize_MG_output
ServerThing.pm  1.90  4 years  olson  Add metabolic_reconstruction to the list of commands sent to the slow queue.
ServicesUtils.pm  1.7  5 months  parrello  Changes copied from SEEDtk project.
Signatures.pm  1.2  7 years  parrello  Various POD fixes.
Sim.pm  1.19  23 months  parrello  Changes copied from SEEDtk project.
Sim2.pm  1.1  6 years  overbeek  tree sims
SimFC.pm  1.3  8 years  overbeek  handle deleted FIDs and failure to get translations
SimsTable.pm  1.11  3 years  golsen  Work around an issue when a user-supplied blast query has a fig| id that is not ...
SproutFIG.pm  1.10  11 years  olson  Added license words.
SproutSearch.pm  1.11  11 years  olson  Added license words.
StandaloneSims.pm  1.1  9 years  olson  FIGM/FIGV changes for sims between RAST orgs.
Stats.pm  1.12  2 years  parrello  Changes copied from SEEDtk project.
StrepRepeats.pm  1.3  4 months  olson  Remove hopefully unused dependencies.
Subsystem.pm  1.156  3 months  olson  Remove carriage returns when saving notes file
SubsystemPrimer.pm  1.8  6 years  overbeek  better help
SubsystemPrimer2SS.pm  1.2  5 years  overbeek  update index
SubsystemProjector.pm  1.1  3 months  parrello  Changes copied from SEEDtk project.
SwissProtUtils.pm  1.1  15 months  golsen  Utilities for converting Swiss-Prot XML to JSON, reading the JSON, and extractin...
TBLstuff.pm  1.2  8 years  overbeek  minor fixes
TableCell.pm  1.1  5 years  golsen  Support for a new sims table format.
TemplateObject.pm  1.8  9 years  parrello  Changed POD format for better compatability with Wiki.
TestUtils.pm  1.12  6 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
ToCall.pm  1.12  6 years  gdpusch  Modified to allow FIGfam IDs with arbitrarily many digits, and to fail safe if F...
Tpn_Int_Reps.pm  1.2  3 years  olson  add sas tag
TraceObject.pm  1.1  3 months  parrello  Changes copied from SEEDtk project.
Tracer.pm  1.137  3 years  olson  Don't change $FIG_Config::temp
TransactionProcessor.pm  1.6  9 years  parrello  Changed POD format for better compatability with Wiki.
TreeFC.pm  1.1  4 years  fangfang  Add module for tree-based functional coupling.
Universal_Seqs.pm  1.1  2 years  jdavis  perl module for finding universal proteins from a peer bork paper
UnvSubsys.pm  1.20  9 years  paczian  added missing "use HTML;"
UpdateServer.pm  1.2  5 years  disz  Remove Sapling stuff`
UserDB.pm  1.2  11 years  olson  Added license words.
UserData.pm  1.6  9 years  parrello  Changed POD format for better compatability with Wiki.
WebColors.pm  1.16  6 years  paczian  re-added circle color scheme
WikiTools.pm  1.8  8 years  parrello  Fixed a glitch in list rendering.
WriteEMBL.pm  1.2  21 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
WriteGenbank.pm  1.2  6 years  gdpusch  Forgot trailing "1;" :(
__init__.py  1.2  11 years  olson  Added license words.
align_and_tree_test.pm  1.1  6 years  golsen  Temp code for using DBMS version of alignment and tree access.
bidir_best_hits.pm  1.3  2 years  golsen  Fix temp file handling to get rid of warning of unsafe usage. The clean up of th...
clustaltree.pm  1.3  8 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
collect_related_sequences.pm  1.6  7 years  golsen  Update to use SeedAware.pm (and do some general clean-up).
compare_coding.pm  1.10  6 years  golsen  Integrate use of SeedAware.pm
crispr.pm  1.10  2 months  parrello  Changes copied from SEEDtk project.
display_related_genomes.pm  1.3  2 years  golsen  Add an alternative function call that is much simpler and cleaner.
fastDNAml.pm  1.2  11 years  olson  Added license words.
ffxtree.pm  1.31  3 years  fangfang  update raxml
find_homologs.pm  1.11  2 years  golsen  Make blast+ the default in find_nucleotide_homologs, solving an issue with occas...
find_special_proteins.pm  1.15  22 months  golsen  Add a few more data to the returned data on matches, and documented.
find_tRNAs.pm  1.1  18 months  golsen  The beginnings of an interface to tRNAscan-SE, with functions for fixing issues ...
gd_tree_0.pm  1.5  7 years  golsen  Extensive reworking of color management.
genome_frequencies.pm  1.3  5 years  golsen  Minor changes to GenomeCodonUsages.pm Add notice that genome_frequencies.pm will...
gjoalign2html.pm  1.11  5 years  golsen  Support for residue color = none.
gjoalignandtree.pm  1.20  4 years  golsen  Add more flexibility ot extract_with_psiblast. Fix most of the temporary file na...
gjoalignment.pm  1.52  2 months  golsen  Added some more functions. Added a cluster option to representative alignment to...
gjoavllib.pm  1.1  3 years  golsen  Some support for clustering and generating representatives of an alignment at an...
gjocluster.pm  1.1  3 years  golsen  Some support for clustering and generating representatives of an alignment at an...
gjocodonlib.pm  1.13  3 years  golsen  Fix the logic so that codon count files created by native_codon_usage() do not g...
gjocolorlib.pm  1.7  6 years  golsen  Added support for luma (HSY color definitions). Changed all code so that html co...
gjocontigs.pm  1.1  2 months  golsen  A new package defining a contigs object that provides random access to DNA seque...
gjogenbank.pm  1.17  2 months  golsen  A few new access functions. Some clarifications.
gjogff.pm  1.3  21 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
gjolib.pm  1.4  6 years  golsen  Make $_ local so that it does not clobber the global value when changed.
gjolists.pm  1.2  10 years  golsen  Updates for cleaner faster code.
gjonativecodonlib.pm  1.4  3 years  golsen  Fix the logic so that codon count files created by native_codon_usage() do not g...
gjonewicklib.pm  1.33  3 years  fangfang  add an option in representative_tips
gjoparseblast.pm  1.11  3 years  golsen  Slightly cleaner version of splitting sequence id and definition.
gjophylip.pm  1.9  6 years  golsen  Fix a cosmetic issue in the cleaning of sequences for PHYLIP.
gjosegmentlib.pm  1.2  6 years  golsen  Forgot the SAS component lines.
gjoseqlib.pm  1.48  2 months  golsen  Several new functions, and added cleaner names for a few commonly used functions...
gjostat.pm  1.6  3 years  golsen  Add more error checking and a median routine.
high_expression_ref_ab.pm  1.1  5 years  golsen  Additional data for codon usage analyses.
match_to_axes.pm  1.3  4 years  golsen  A more radical solution to making this module obsolete. Use CodonUsageTable.pm i...
model.pm  1.36  6 years  dejongh  change scenario handling to use path_info.txt
overlap_resolution.pm  1.9  2 weeks  olson  Fix score and qual check for seleno/pyrrolysoproteins.
proml.pm  1.10  4 years  golsen  Change tempoary file names and locations to be more robust.
protdist_neighbor.pm  1.2  6 years  golsen  Make $_ local so that it does not clobber the global value when changed.
pyrrolysylprotein_ref_seq.pm  1.2  5 years  olson  Make these SAS components
raedraw.pm  1.14  9 years  parrello  Changed POD heading levels.
raelib.pm  1.47  4 years  redwards  adding phage stuff
representative_sequences.pm  1.22  4 years  golsen  Some minor improvements in code and documentations (comments).
selenoprotein_ref_seq.pm  1.7  5 years  olson  Make these SAS components
set_utilities.pm  1.3  7 years  overbeek  make SAS components
tree_neighborhood.pm  1.1  10 years  overbeek  add tree_neighbors and latest phylogeny stuff
tree_utilities.pm  1.24  7 months  overbeek  fix tree_utilities parser

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3