 Parent Directory
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tests/
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Export/
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tree_utilities.pm
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1.20 |
10 years |
olson |
Add more modules to the SAS toolkit.
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tree_neighborhood.pm
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1.1 |
12 years |
overbeek |
add tree_neighbors and latest phylogeny stuff
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set_utilities.pm
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1.3 |
9 years |
overbeek |
make SAS components
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selenoprotein_ref_seq.pm
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1.5 |
9 years |
golsen |
Add some reference sequences and replace ; with @ in functions.
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representative_sequences.pm
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1.18 |
8 years |
golsen |
Huge restructuring of the rep_seq() and rep_seq2() functions. Better performanc... |
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raelib.pm
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1.45 |
8 years |
redwards |
adding a pegs in order method (should probably be in FIG.pm cos way useful)
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raedraw.pm
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1.14 |
11 years |
parrello |
Changed POD heading levels.
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pyrrolysylprotein_ref_seq.pm
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1.1 |
12 years |
golsen |
Add support for pyrrolysyl proteins. Also, major revision and clean-up
of the t... |
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protdist_neighbor.pm
|
1.1 |
12 years |
golsen |
A package for protdist and neighbor PHYLIP trees.
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proml.pm
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1.9 |
9 years |
golsen |
Minor updates to SEED awareness.
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model.pm
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1.36 |
8 years |
dejongh |
change scenario handling to use path_info.txt
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gjostat.pm
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1.3 |
9 years |
golsen |
Convert die to confess.
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gjoseqlib.pm
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1.25 |
8 years |
golsen |
Just some additions to the function descriptions.
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gjosegmentlib.pm
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1.2 |
8 years |
golsen |
Forgot the SAS component lines.
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gjophylip.pm
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1.9 |
8 years |
golsen |
Fix a cosmetic issue in the cleaning of sequences for PHYLIP.
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gjoparseblast.pm
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1.8 |
9 years |
golsen |
Fix two minor typographical errors in the documentation.
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gjonewicklib.pm
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1.25 |
9 years |
golsen |
Change behavior of reroot_tree() to ignore distance if there is only one
node.
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gjonativecodonlib.pm
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1.2 |
8 years |
golsen |
Forgot the SAS component lines.
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gjolists.pm
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1.2 |
12 years |
golsen |
Updates for cleaner faster code.
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gjolib.pm
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1.3 |
10 years |
olson |
Add more modules to the SAS toolkit.
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gjogff.pm
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1.2 |
8 years |
golsen |
Changes to fix some bugs in GenBank format reading and writing.
Changes to deal ... |
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gjogenbank.pm
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1.9 |
8 years |
golsen |
Some sites do not include a blank space after "ORIGIN".
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gjocolorlib.pm
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1.7 |
9 years |
golsen |
Added support for luma (HSY color definitions).
Changed all code so that html co... |
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gjocodonlib.pm
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1.2 |
8 years |
golsen |
Forgot the SAS component lines.
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gjoalignment.pm
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1.38 |
8 years |
fangfang |
update align_with_mafft
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gjoalignandtree.pm
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1.16 |
8 years |
golsen |
Minor consistency improvements in options, and remove redundancy in getting
the ... |
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gjoalign2html.pm
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1.5 |
9 years |
fangfang |
SAS component
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gd_tree_0.pm
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1.5 |
9 years |
golsen |
Extensive reworking of color management.
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find_special_proteins.pm
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1.12 |
9 years |
olson |
typod the declaration
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find_homologs.pm
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1.4 |
8 years |
golsen |
use SeedAware
Many changes in details of code.
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ffxtree.pm
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1.24 |
8 years |
fangfang |
fixed a format issue with description field in tree_to_html
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fastDNAml.pm
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1.2 |
14 years |
olson |
Added license words.
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display_related_genomes.pm
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1.2 |
9 years |
golsen |
Minor documentation changes in code.
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compare_coding.pm
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1.10 |
8 years |
golsen |
Integrate use of SeedAware.pm
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collect_related_sequences.pm
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1.6 |
9 years |
golsen |
Update to use SeedAware.pm (and do some general clean-up).
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clustaltree.pm
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1.3 |
10 years |
golsen |
New super duper ala Peter T. Hooper paralog resolution interface.
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__init__.py
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1.2 |
14 years |
olson |
Added license words.
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WriteGenbank.pm
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1.2 |
8 years |
gdpusch |
Forgot trailing "1;" :(
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WikiTools.pm
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1.8 |
10 years |
parrello |
Fixed a glitch in list rendering.
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WebColors.pm
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1.16 |
8 years |
paczian |
re-added circle color scheme
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UserData.pm
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1.6 |
12 years |
parrello |
Changed POD format for better compatability with Wiki.
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UserDB.pm
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1.2 |
14 years |
olson |
Added license words.
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UnvSubsys.pm
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1.20 |
11 years |
paczian |
added missing "use HTML;"
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TransactionProcessor.pm
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1.6 |
12 years |
parrello |
Changed POD format for better compatability with Wiki.
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Tracer.pm
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1.132 |
8 years |
parrello |
Added an option to display configuration data to the command-line setup utility.... |
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ToCall.pm
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1.11 |
10 years |
gdpusch |
Major rewrite to prevent already-found PEGs from being re-called by every stage ... |
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TestUtils.pm
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1.11 |
10 years |
parrello |
Fixed display glitch for pure white space.
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TemplateObject.pm
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1.8 |
12 years |
parrello |
Changed POD format for better compatability with Wiki.
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TBLstuff.pm
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1.2 |
10 years |
overbeek |
minor fixes
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Subsystem.pm
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1.149 |
8 years |
olson |
Subsystem speedup fixes.
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Stats.pm
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1.8 |
10 years |
parrello |
Added a method to extract saved messages.
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StandaloneSims.pm
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1.1 |
11 years |
olson |
FIGM/FIGV changes for sims between RAST orgs.
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SproutSearch.pm
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1.11 |
14 years |
olson |
Added license words.
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SproutFIG.pm
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1.10 |
14 years |
olson |
Added license words.
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SimFC.pm
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1.3 |
10 years |
overbeek |
handle deleted FIDs and failure to get translations
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Sim2.pm
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1.1 |
8 years |
overbeek |
tree sims
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Sim.pm
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1.14 |
10 years |
olson |
Distro fixups
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Signatures.pm
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1.2 |
9 years |
parrello |
Various POD fixes.
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ServerThing.pm
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1.73 |
8 years |
parrello |
New method for features expressed in a given fraction of the experiments.
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ServerScripts.pm
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1.5 |
9 years |
overbeek |
add summarize_MG_output
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SeedV.pm
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1.9 |
9 years |
gdpusch |
Changed a debugging line to print to STDERR, not STDOUT; print only if VERBOSE.
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SeedUtils.pm
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1.61 |
8 years |
overbeek |
delete comments before testing for hypo
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SeedSims.pm
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1.1 |
10 years |
overbeek |
additions to support partitioning of sims
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SeedHTML.pm
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1.3 |
10 years |
olson |
More distro fixes.
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SeedEnv.pm
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1.4 |
8 years |
olson |
Use new path to FBAModelSerer
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SeedDas.pm
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1.22 |
12 years |
parrello |
Removed a FIG dependency that was causing duplicate-method warnings.
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SeedAware.pm
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1.7 |
8 years |
olson |
add win32 support to executable_For
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ScriptThing.pm
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1.8 |
9 years |
parrello |
Expression vector support methods.
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Scenario.pm
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1.10 |
8 years |
dejongh |
change scenario handling to use path_info.txt
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SapCompareRegions.pm
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1.3 |
8 years |
olson |
Change to output format; outer hash with fid => results, rows are now hashes
wit... |
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SampleDir.pm
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1.4 |
9 years |
olson |
More analysis fixes; user-agent setting.
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SameFunc.pm
|
1.17 |
12 years |
overbeek |
fix to SameFunc.pm
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SUPserver.pm
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1.1 |
9 years |
parrello |
New Sapling update support.
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SUP.pm
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1.2 |
9 years |
parrello |
New methods for alignment data.
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SSserver.pm
|
1.17 |
10 years |
parrello |
Removed from the SAS distribution.
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SSU_rRNA_reps.pm
|
1.3 |
9 years |
golsen |
Adjust end of one reference sequence by padding it slightly.
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SS.pm
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1.13 |
10 years |
parrello |
More documentation cleanup.
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SFXlate.pm
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1.119 |
10 years |
parrello |
Added "families_containing_peg".
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SAPtutorial.pm
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1.10 |
9 years |
parrello |
Fixed some errors in examples of ID types.
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SAPserver.pm
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1.14 |
9 years |
parrello |
Support for local SQLite servers.
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SAP.pm
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1.158 |
8 years |
parrello |
Added new method to compute reaction paths.
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RemoteCustomAttributes.pm
|
1.8 |
12 years |
parrello |
Changed POD format for better compatability with Wiki.
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ReactionPath.pm
|
1.1 |
8 years |
parrello |
Added new method to compute reaction paths.
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README
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1.1.1.1 |
16 years |
efrank |
import
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RC.pm
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1.2 |
14 years |
olson |
Added license words.
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RASTserver.pm
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1.23 |
9 years |
gdpusch |
Fixed bugs in and added more support for Viral and Euk jobs.
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RAST_submission.pm
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1.28 |
8 years |
olson |
typofix
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Quality.pm
|
1.6 |
12 years |
parrello |
Changed POD format for better compatability with Wiki.
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ProtSims.pm
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1.19 |
8 years |
overbeek |
turn off debugging print
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ProtFamsLite.pm
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1.2 |
10 years |
arodri7 |
added functions and made functions work
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ProtFams.pm
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1.3 |
10 years |
arodri7 |
added functions and made functions work
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ProtFamLite.pm
|
1.2 |
10 years |
arodri7 |
added functions and made functions work
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PinnedRegions.pm
|
1.34 |
9 years |
olson |
fix unlink here too
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PickFeatureSet.pm
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1.2 |
10 years |
overbeek |
add .html to HTML files
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Phage.pm
|
1.3 |
9 years |
redwards |
minor correction
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PartitionSeqs.pm
|
1.3 |
10 years |
overbeek |
return either scalar or list
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ParalogResolution.pm
|
1.5 |
10 years |
golsen |
Modifications to support line-drawing character set in tree printer plots.
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PageBuilder.pm
|
1.14 |
12 years |
parrello |
Changed POD format for better compatability with Wiki.
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PHOB.pm
|
1.15 |
10 years |
overbeek |
switch from clustalw to muscle
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P2Pupdate.pm
|
1.62 |
11 years |
golsen |
Move writing of assignment annotation from a case-by-case basis (and it
was miss... |
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P2P.pm
|
1.31 |
14 years |
olson |
Added license words.
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Overlap.pm
|
1.4 |
12 years |
parrello |
Changed POD format for better compatability with Wiki.
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OddStarts_ref.pm
|
1.1 |
11 years |
overbeek |
add the ability to find TIF3
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Observation.pm
|
1.83 |
8 years |
redwards |
correcting web links
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NewGenome.pm
|
1.80 |
10 years |
parrello |
Protected a "new FIG" in open code with an eval. THIS MUST BE FIXED.
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NRTools.pm
|
1.4 |
10 years |
olson |
update to new metadata standard
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NCBI_taxonomy.pm
|
1.4 |
8 years |
golsen |
Add more formats in which abbreviated lineages can be returned.
Add long form of... |
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NCBI_genetic_code.pm
|
1.3 |
9 years |
olson |
add SAS header
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MinimalTracer.pm
|
1.1 |
9 years |
olson |
More FS_RAST modes & supporting code for SAS use.
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MgRastSims.pm
|
1.1 |
10 years |
redwards |
a new package for getting sims for the mg-rast
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MetaSubsystem.pm
|
1.4 |
11 years |
bartels |
added functions for genome manipulation
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MergeTransactions.pm
|
1.3 |
12 years |
parrello |
Changed POD format for better compatability with Wiki.
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Markups.pm
|
1.2 |
12 years |
parrello |
Changed POD format for better compatability with Wiki.
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MapIDs.pm
|
1.1 |
12 years |
wilke |
Initial version of functions to map different ids
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Makefile
|
1.13 |
9 years |
gdpusch |
Initial checkin of module to facilitate writeing GenBank output.
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LogReader.pm
|
1.1 |
11 years |
parrello |
Added to facilitate reading the error log.
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ListServerScripts.pm
|
1.2 |
8 years |
parrello |
Fixed to point to PUBSEED server for documentation.
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KmersOld.pm
|
1.1 |
10 years |
olson |
version of Kmers.pm before the argument changes; made to go with figfam_server_2... |
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Kmers.pm
|
1.28 |
9 years |
olson |
fix off-by-one
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KGMLData.pm
|
1.4 |
12 years |
dejongh |
Hope College updates
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KGML.pm
|
1.4 |
12 years |
olson |
Hope college modifications.
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JobScheduler.pm
|
1.10 |
8 years |
olson |
Put.
The Scheduler.
Back.
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InterfaceRoutines.pm
|
1.12 |
13 years |
olson |
readonly fixes; seed-run-job update to run from input file
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InsertIntoTree.pm
|
1.15 |
12 years |
overbeek |
check figfams fixes
|
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HtmlPageParser.pm
|
1.2 |
14 years |
olson |
Added license words.
|
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HTML.py
|
1.6 |
14 years |
olson |
Added license words.
|
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HTML.pm
|
1.130 |
10 years |
arodri7 |
added links to set_prot_links
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GenomeMetaDatabase.pm
|
1.1 |
10 years |
jared |
*** empty log message ***
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GenomeMetaDB.pm
|
1.5 |
10 years |
jared |
added update_path
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GenomeMeta.pm
|
1.16 |
9 years |
olson |
Add lock retries; probably not needed now that I think I've fixed FileLocking bu... |
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GenomeLists.pm
|
1.2 |
11 years |
bartels |
put in verify_dir so that the directory is produced automatically
if you access ... |
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GenomeIDMap.pm
|
1.4 |
14 years |
olson |
Added license words.
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GenoGraphics.pm
|
1.24 |
9 years |
golsen |
Back pedal on the attempt to diagnose jpeg and png availability in GenoGraphics
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FullLocation.pm
|
1.25 |
10 years |
parrello |
Added a method to compute the total location length.
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FudgeTransactions.pm
|
1.4 |
12 years |
parrello |
Changed POD format for better compatability with Wiki.
|
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FileLocking.pm
|
1.4 |
9 years |
olson |
Changes for DesktopRast.
CVHnS: ------------------------------------------------... |
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FigGFF.pm
|
1.22 |
12 years |
redwards |
Rewritten gff2tab and updated FigGFF POD/methods
|
|
FS_RAST.pm
|
1.35 |
8 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 |
12 years |
golsen |
Improve handling of multidomain query sequences in coloring of sims
matches (do ... |
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FIG_CGI.pm
|
1.11 |
11 years |
olson |
Add annotation support to FIGV. Add FIGM.
|
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FIGV.pm
|
1.97 |
8 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
|
1.19 |
8 years |
olson |
Don't bail on creating a FIGM if one of hte FIGV creations fails.
|
|
FIGGenDB.pm
|
1.6 |
14 years |
olson |
Added license words.
|
|
FIGAttributes.pm
|
1.4 |
10 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
|
1.839 |
8 years |
redwards |
correcting usable subsystems
|
|
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 |
8 years |
olson |
Support for duplicate match removal.
Support for using Subsystems/{bindings,subs... |
|
ErrorMessage.pm
|
1.2 |
9 years |
olson |
remove unused use CGI.
|
|
DocUtils.pm
|
1.18 |
10 years |
parrello |
Added documentation functions to the Sapling server.
|
|
Diagram.pm
|
1.19 |
8 years |
redwards |
fixing jpeg images
|
|
DBrtns.pm
|
1.27 |
13 years |
overbeek |
Fix extra-args option to go at teh start of the list.
|
|
DBKernel.pm
|
1.65 |
8 years |
olson |
Caching / FCGI speedup modifications.
|
|
CorrespondenceCache.pm
|
1.2 |
8 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 |
10 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 |
10 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
|
1.24 |
8 years |
olson |
Add 500 to the list of error codes to retry for
|
|
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 |
13 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 |
11 years |
golsen |
Two subroutines to support a user ordering of items. Created for the
compare ge... |
|
Blast.pm
|
1.5 |
11 years |
overbeek |
close TMP files in Blast.pm
|
|
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
|
1.19 |
10 years |
parrello |
Updated to Sapling Server for Berkeley.
|
|
BadCall.pm
|
1.4 |
11 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 |
11 years |
parrello |
Added a TITLE statement for the Wiki.
|
|
AnnoClearinghouse.pm
|
1.44 |
10 years |
wilke |
Modified sql query to ? syntax
|
|
AlignsAndTreesServer.pm
|
1.3 |
8 years |
overbeek |
debugged
|
|
AlignsAndTrees.pm
|
1.4 |
8 years |
overbeek |
debugged
|
|
AlignTree.pm
|
1.38 |
8 years |
fangfang |
added function for extracting conserved regions from alignment
|
|
AliasAnalysis.pm
|
1.11 |
8 years |
parrello |
Updates for single-genome loader.
|
|
AliTrees.pm
|
1.4 |
12 years |
overbeek |
fix AliTrees.pm to fail gracefully
|
|
AliTreeSims.pm
|
1.6 |
8 years |
fangfang |
remove old code
|
|
AliTreeIdConvert.pm
|
1.1 |
8 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 |
8 years |
fangfang |
add blast function
|
|
ANNOserver.pm
|
1.20 |
9 years |
parrello |
Fixed a POD error.
|
|
ANNO.pm
|
1.9 |
8 years |
parrello |
Fixed missing method problem.
|
|
ALITREserver.pm
|
1.1 |
8 years |
parrello |
New alignment/tree server stuff.
|
|
ALITRE.pm
|
1.1 |
8 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
|
