| 2005-09-27 |
jason | remove debugging crap
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commit | commitdiff | tree |
| 2005-09-27 |
jason | whoops, inc test count too
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commit | commitdiff | tree |
| 2005-09-27 |
jason | test repeat masker on different versions, this probably...
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commit | commitdiff | tree |
| 2005-09-27 |
jason | cleanup after oneself
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commit | commitdiff | tree |
| 2005-09-27 |
jason | skip where appropriate
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commit | commitdiff | tree |
| 2005-09-27 |
jason | work on diff versions of MUSCLE
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commit | commitdiff | tree |
| 2005-09-27 |
jason | more flexible version matching for percid
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commit | commitdiff | tree |
| 2005-09-27 |
jason | test for wise 2.2.0 and 2.2.3
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commit | commitdiff | tree |
| 2005-09-27 |
jason | simplify java version lookup
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commit | commitdiff | tree |
| 2005-09-27 |
jason | George Hartzell's excellent code fixes
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commit | commitdiff | tree |
| 2005-09-27 |
jason | update test nums and added a test; per George Hartzell
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commit | commitdiff | tree |
| 2005-09-27 |
jason | add some POD, note that this module is probably incomplete
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commit | commitdiff | tree |
| 2005-09-26 |
jason | strike that, emboss 2.8.0 is where the cutoff in argument...
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commit | commitdiff | tree |
| 2005-09-26 |
jason | EMBOSS 3.0.0 testing passes
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commit | commitdiff | tree |
| 2005-09-25 |
jason | adhere to the style that makes sense to me
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commit | commitdiff | tree |
| 2005-09-25 |
jason | genewise test files
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commit | commitdiff | tree |
| 2005-09-25 |
jason | genewise tests should pass now on 2.2.3 and 2.2.0
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commit | commitdiff | tree |
| 2005-09-25 |
jason | an hour of my life gone... pseudowise wrapper is now...
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commit | commitdiff | tree |
| 2005-09-25 |
jason | silence undef warning
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commit | commitdiff | tree |
| 2005-09-25 |
jason | more relaxed percent id checking, this is probably...
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commit | commitdiff | tree |
| 2005-09-25 |
jason | profile align expects 1st arg to be profile, second...
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commit | commitdiff | tree |
| 2005-09-25 |
jason | up to 1775 not 1776
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commit | commitdiff | tree |
| 2005-09-25 |
jason | Tcoffee --> MAFFT, version stuff removed, allow percent...
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commit | commitdiff | tree |
| 2005-09-25 |
jason | needed test files
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commit | commitdiff | tree |
| 2005-09-22 |
jason | properly run Exonerate
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commit | commitdiff | tree |
| 2005-09-22 |
jason | test rev com too
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commit | commitdiff | tree |
| 2005-09-22 |
jason | more robust test for exonerate (vulgar only really...
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commit | commitdiff | tree |
| 2005-06-16 |
jason | support for the soon-to-be-released update cmdline...
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commit | commitdiff | tree |
| 2005-06-16 |
jason | test more muscle args, fix new {} _rearrage with mixed...
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commit | commitdiff | tree |
| 2005-05-16 |
jason | small cosmetic changes
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commit | commitdiff | tree |
| 2005-05-12 |
jason | POD changes
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commit | commitdiff | tree |
| 2005-04-27 |
jason | switch flag per bug #1775
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commit | commitdiff | tree |
| 2005-04-24 |
jason | operate happily with new open-version
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commit | commitdiff | tree |
| 2005-04-18 |
jason | Scott Markel's additions + some tweaking for hmmalign...
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commit | commitdiff | tree |
| 2005-04-18 |
jason | Scott Markel's additions + some tweaking for hmmalign
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commit | commitdiff | tree |
| 2005-03-30 |
jason | allow omega to varied
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commit | commitdiff | tree |
| 2004-12-16 |
jason | executable is the string to run
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commit | commitdiff | tree |
| 2004-11-20 |
jason | LVB changes by Daniel
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commit | commitdiff | tree |
| 2004-11-20 |
jason | add Baseml
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commit | commitdiff | tree |
| 2004-11-20 |
jason | update doc
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commit | commitdiff | tree |
| 2004-11-16 |
jason | fix filehandle problem without using IO::String --...
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commit | commitdiff | tree |
| 2004-11-16 |
jason | doc fix
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commit | commitdiff | tree |
| 2004-11-16 |
jason | skip out when exonerate is not installed
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commit | commitdiff | tree |
| 2004-11-16 |
jason | skip tests properly on no Blat installed
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commit | commitdiff | tree |
| 2004-11-16 |
jason | cleanup code for debugging
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commit | commitdiff | tree |
| 2004-11-16 |
jason | revision string fix
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commit | commitdiff | tree |
| 2004-11-16 |
jason | fix revision string problems
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commit | commitdiff | tree |
| 2004-10-01 |
jason | support primer3 or primer3_core as app name with a...
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commit | commitdiff | tree |
| 2004-10-01 |
jason | Some code formatting
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commit | commitdiff | tree |
| 2004-10-01 |
jason | update link
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commit | commitdiff | tree |
| 2004-10-01 |
jason | debugging enabled
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commit | commitdiff | tree |
| 2004-10-01 |
jason | test can support PAML 3.14 now
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commit | commitdiff | tree |
| 2004-07-26 |
jason | some docu update
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commit | commitdiff | tree |
| 2004-07-26 |
jason | allow alignment to be passed in to run()
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commit | commitdiff | tree |
| 2004-07-12 |
jason | some Documentation fixes to clarify how to set the...
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commit | commitdiff | tree |
| 2004-07-12 |
jason | Bare Bones MUSCLE wrapper and tests
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commit | commitdiff | tree |
| 2004-07-10 |
jason | allow alignment to be specified in run()
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commit | commitdiff | tree |
| 2004-07-09 |
jason | support more models
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commit | commitdiff | tree |
| 2004-06-30 |
jason | bug #1646; This should go with msf if gcg format is...
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commit | commitdiff | tree |
| 2004-06-30 |
jason | allow alignment methods (A=[01234]) to be specified...
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commit | commitdiff | tree |
| 2004-06-24 |
jason | let alpha be more free - don't try and restrict it
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commit | commitdiff | tree |
| 2004-06-24 |
jason | tests more resistant to rounding differences
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commit | commitdiff | tree |
| 2004-06-24 |
jason | This still needs an overhaul but fix minor doc bugs...
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commit | commitdiff | tree |
| 2004-06-24 |
jason | attempted cleanup of code for bug #1657
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commit | commitdiff | tree |
| 2004-06-02 |
jason | get rid of deprecation warning
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commit | commitdiff | tree |
| 2004-05-14 |
jason | small docu fixes
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commit | commitdiff | tree |
| 2004-05-14 |
jason | more, better tests for the new implementation for tree...
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commit | commitdiff | tree |
| 2004-02-20 |
jason | allow 0 value attributes per Susan Miller's bug report
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commit | commitdiff | tree |
| 2004-02-05 |
jason | adding Daniel's LVB wrapper
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commit | commitdiff | tree |
| 2004-01-02 |
jason | docfix, an array of genes can be returned
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commit | commitdiff | tree |
| 2003-12-30 |
jason | docu fix
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commit | commitdiff | tree |
| 2003-12-17 |
jason | stupid jason - it saves a syscall
stupid jason - it saves a syscall
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commit | commitdiff | tree |
| 2003-12-17 |
jason | what is that underscore in there for?
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commit | commitdiff | tree |
| 2003-12-17 |
jason | catfile not catdir
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commit | commitdiff | tree |
| 2003-11-19 |
jason | George Hartzell fixes
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commit | commitdiff | tree |
| 2003-09-30 |
jason | use save_tempfiles, use PROGRAMNAME as a variable,...
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commit | commitdiff | tree |
| 2003-09-30 |
jason | typo
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commit | commitdiff | tree |
| 2003-09-08 |
jason | default should be an arrayref
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commit | commitdiff | tree |
| 2003-09-03 |
jason | wait -this isn't necessary , we already pad the PROGRAMNAME...
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commit | commitdiff | tree |
| 2003-09-03 |
jason | bug #1507 add MSwin .exe extension where appropriate
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commit | commitdiff | tree |
| 2003-09-03 |
jason | bug #1507, SYNOPSIS is runnable now with API changes
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commit | commitdiff | tree |
| 2003-08-14 |
jason | can't declare are expect a variable at the same time
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commit | commitdiff | tree |
| 2003-08-14 |
jason | no need for this debugging
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commit | commitdiff | tree |
| 2003-08-14 |
jason | fix stupidity with tempfilehandle and outfh not being...
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commit | commitdiff | tree |
| 2003-07-11 |
jason | align the code
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commit | commitdiff | tree |
| 2003-07-11 |
jason | properly get the hash value
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commit | commitdiff | tree |
| 2003-06-28 |
jason | Mark Wagner's enhancements bug #1399
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commit | commitdiff | tree |
| 2003-05-30 |
jason | POD fixes
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commit | commitdiff | tree |
| 2003-05-21 |
jason | some code cleanup to avoid warnings and insure filehandles...
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commit | commitdiff | tree |
| 2003-05-21 |
jason | more modern use of hit/query instead of feature1/feature2...
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commit | commitdiff | tree |
| 2003-03-29 |
jason | begin documenting the necessary env variables
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commit | commitdiff | tree |
| 2003-03-29 |
jason | remove debugging code
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commit | commitdiff | tree |
| 2003-03-29 |
jason | update error message
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commit | commitdiff | tree |
| 2003-03-28 |
jason | rework tempfile handling to explicitly close a filehanle...
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commit | commitdiff | tree |
| 2003-03-28 |
jason | Handle interleaved output from phylip 3.6, handle 3...
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commit | commitdiff | tree |
| 2003-03-28 |
jason | test quiet
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commit | commitdiff | tree |
| 2003-03-24 |
jason | some scripts for running protdist and neighbor, for...
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commit | commitdiff | tree |
| 2003-03-23 |
jason | require jumble parameter to be odd or we get ina bad...
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commit | commitdiff | tree |
| 2003-03-17 |
jason | bug which was not caught before
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commit | commitdiff | tree |
| 2003-03-14 |
jason | test needs to be in same CVS module as the perl module
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commit | commitdiff | tree |
