POY5.0.1 alpha release

[Ward Wheeler]

POY users,

We are please to announce the release of  the POY5.0.1 alpha.  This is

mainly a big fix release.

Windows and OSX Binaries, source, and documentation are available 

at http://research.amnh.org/scicomp/projects/poy.php.

The emphasis of this release is functionality, with efficiency a major goal 

as we move through the pre-release stages.

As always, please contact us with bug reports and suggestions.

Enjoy,

The POY5 Team

CHANGES BETWEEN 5.0.0a and 5.0.1a

New Features:
    - orientation set to true by default for breakinversion data-type.
    - faster alignment under low-mem settings

Bugs Fixed:
    - Fixed Makfile in src directory to perform the install, and removed the
      Makefile/configuration in the root directory. These files were synonyms
      for the ones the src directory and add no value to the compilation
      process.
    - Default for configuring with --enable-mpi is to set interface to flat.
      This is a requirement that is oft forgotten and there is no reason why we
      cannot facilitate that requirement. Setting interface to anything else
      will over-write that choice and report a warning.
    - Add Error message for input sequence with different number of
      fragments(fragments are devided by '#').  (bug report by Torsten Dikow).
    - Improved Makefile and Configure scripts from minor errors. Also removed
      Makefile and configure script from the root directory to avoid confusion
      and easier to maintain. (bug report by Jan De Laet).
    - Report lkmodel (to report likelihood model), was not working properly in
      certain situations; without identifiers.  (bug report by John Denton).
    - Transform likelihood with multiple types (for example a combination of
      static and dynamic) would fail in the transform due to alphabet size
      issues. We partition the data now between static and dynamic and then
      apply the transform to the characters. (bug report by Fernando Marques).
    - Used non-affine alignment for affine models under parsimony; this has
      been reverted correctly, and also includes affine low-mem ukkonen.
    - Compiling supramap and cmxs libraries dynamic linking rule was missing
      in our myocamlbuild file. (bug report by Travis Treseder).
    - Diagnosing Static and Dynamic Likelihood mixed models caused errors due to
      demarcation of sets of data. Resolved so we group by the type of model
      being applied to the characters as well as pre-defined sets and data
      classes.
    - Diagnosis for Dynamic Likelihood characters did not work on leaf nodes.
    - Backtrace works the same in POY4 and POY5 for normal alignment; the issue
      is in regard to the preference in inserting indels in which sequence.
    - Affine alignment bug with aligning two sequences at a point each having 
      gap polymorphisms. This is a very rare instance.

New Commands:
    - set(space_saving_alignment)
    - set(normal_alignment)
        - commands turn on/off low-memory alignment procedure. Default off.

Changed Commands:
    - transform(chromosome:(newkkonen,..)
    - transform(genome:(newkkonen,... ))
        - this option is specified in the low-memory/space-saving alignment
          procedure mentioned above.

--
Ward Wheeler
Division of Invertebrate Zoology
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024-5192
USA
whe...@amnh.org
http://research.amnh.org/scicomp/ward_wheeler.html