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Commits on Dec 15, 2009

• Merging

  

  Andres Varon

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• Merged.

  

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Commits on Aug 3, 2009

• Merged

  

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Commits on Jul 9, 2009

• Merged

  

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Commits on Jul 8, 2009

• Merged

  

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Commits on Mar 16, 2009

• Removed debugging message left by mistake in the configure script.

  

  Andres Varon

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• Corrected errors in sed command line that caused bogus test failures.

  

  Andres Varon

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• Corrected errors in sed command line that caused bogus test failures.

  

  Andres Varon

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• Enclosed sed commands in quotes to avoid test errors in some architectures.

  

  Andres Varon

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• Enclosed sed commands in quotes to avoid test errors in some architectures.

  

  Andres Varon

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• Enabled the xslt-config tests to the windows port in configure script.

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  Andres Varon

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Commits on Mar 13, 2009

• Fixed error for tests in honey due to missing quotes in VERSION rule.

  

  Andres Varon

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  a7d3a2d

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• Corrected transplant error from 4.1.2 branch in configuration files.

  

  Andres Varon

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• Minor update in the INSTALL instructions to the new ocamlbuild targets.

  

  Andres Varon

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  4ebea2d

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• Removed the empty file NEWS.

  

  Andres Varon

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  7a37641

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• Removed the empty file NEWS.

  

  Andres Varon

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  6a6c804

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• Updated the text execution to call poy_test.native instead of the old target.

  

  Andres Varon

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  c2f8b7d

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• Updated the text execution to call poy_test.native instead of the old target.

  

  Andres Varon

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  55c8b2a

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• Major cleanup of dead files and updated the test engine target for ocamlbuild.

  

  Andres Varon

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  209937f

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• Major cleanup of dead files and updated the test engine target for ocamlbuild.

  

  Andres Varon

  committed
  0db162e

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• Merged.

  

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• Merged.

  

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Commits on Mar 11, 2009

• Replaced the build system with ocamlbuild.

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  Andres Varon

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Commits on Feb 24, 2009

• Added a note clarifying that root:"name" is the taxon name in tutorial 4.1.

  

  Andres Varon

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Commits on Feb 4, 2009

• Added the benchmarks to compare POY's results with prealigned sequences.

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  Andres Varon

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Commits on Feb 3, 2009

• Commented out the partitioned commands which are not ready for the public.

  

  Andres Varon

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Commits on Jan 30, 2009

• Added neighbor joining as build method (build (nj)).

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  Andres Varon

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• Removed an unused variable that caused a warning at compilation time.

  

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Commits on Jan 29, 2009

• Added swap_algorithms to benchmark a number of swap algorithms in parallel.

  

  Andres Varon

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• Reduced the number of annealing benchmarks to make them feasible.

  

  Andres Varon

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• Added the swap_annealing program for benchmarking simmulated annealing.

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  Andres Varon

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Commits on Jan 28, 2009

• Added read (praligned:(..., gap_opening:x)). See the program documentation.

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  Andres Varon

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Commits on Jan 27, 2009

• Added the build_benchmark program to test different build algorithms.

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  Andres Varon

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