POY5-alpha release

[Ward C Wheeler]

POY users,

We are please to announce the initial alpha release of POY5.  Many new features 

have been added  and others improved including maximum likelihood, chromosomal, 

and genomic analysis. 

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 4.1.2.1 and 5.0.0

New Features

    - Added likelihood criterion for diagnosing trees.

        - Added methods of optimization for likelihood during build/swap/fuse

        - Support for dynamic and static characters under a variety of models.

        - Most Parsimonious and Maximum Average Likelihood cost models.

        - Static and Dynamic character support for likelihood, including any

          alphabet size (ie, discrete morphological characters, amino acid, ...)

    - Added a variety of median solvers for rearrangements.

    - Support for Genome and Chromosome characters with annotator Mauve.

    - New selection method for polymorphic data in fixed state characters.

    - Added level support on all alphabets sizes.

    - Changed default TCM to 1,1.

    - Updated configure scripts for newer versions of gcc and ocaml.

    - Low memory option for alignment of sequences.

    - Changed command for transform for dealing with identifiers.

    - Require one type of delimiters in data files.

    - Choice of equally costly medians can be user specified.

    - pre-aligned for custom-alphabet and amino-acid characters.

    - Allow additional medians by search-based command for fixed state

      characters.

    - Internal assignment in diagnosis output of fixed state characters print

      taxon name.

    - Default for amino-acid to not use 3D alignment in up-pass

    - Better support for manipulating and calling character sets in data

    - Graphic output for mauve outlining alignment of blocks and rearrangements

Bugs Fixed:

    - Memory leaks in grappa interface.

    - Building random trees does not use a modified Wagner build.

    - Missing data is presented as a '?' in output from implied alignments.

    - Avoid rediagnosing trees before certain operations.

    - Issues in reading prealigned phylip files.

    - Better support for all features of NEXUS files.

        - Added POY block to nexus files for our specific needs, including

          likelihood, chromosome, genome, and dynamic character information.

    - Detecting file types is more accurate.

    - Parsing file types has better support.

    - Can transform Break Inversion and Custom alphabet with cost matrix file.

    - Replaced command dynamic_pam to deal with new datatypes.

        - now chromosome, genome, breakinv, etc.

    - Priority for backtrace in the alignments standardized between floating

      point alignment (dynamic likelihood), affine, and sequence characters.

    - Nexus output is fully produced when called in the report command

      --includes trees, set information, data, etc.

    - Support for scientific notation of floating point numbers in parsers.

    - Custom Alphabet and Break Inversion data characters case sensitive.

    - Fixed and improved POY help documentation 

    - Initial cost for downpass in fixed state characters was incorrect (up-pass

      and final costs were correct).

    - Status messages during branch and bound build (after every 1% complete).

    - 3D option set to false is observed after re-diagnosis.

    - all element code (X) in amino acid is treated as a polymorphism

    - Improved max_time behavior in searching

    - Fixed cost issue in rearrangement for annotated characters

Features eliminated:

    - dynamic_pam command has been replaced by the commands chromosome, genome,

      breakinv, and custom_alphabet.

New Commands:

    - transform( likelihood:( ... ) )

    - transform( genome:( ... ) )

    - transform( chromosome:( ... ) )

    - transform( breakinv:( ... ) )

    - transform( custom_alphabet:( ... ) )

    - transform( parsimony )

    - transform( level:INT )

    - set( partition:( ... ))

    - set( codon_partition:( ... ))

    - swap/fuse/build( optimize:(model:(...),branches:(...)) )

    - report( trees:(branches) )

    - report( lkmodel )

Changed Commands:

    - transform( [IDS], (transformations,...) )

    - read( custom_alphabet:([datafile],[costmatrix],[prealigned]))

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

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

[jan.d...@skynet.be]

Hi Ward,

Just to let you know that the default './configure' on an Ubuntu 11.10
system (with gcc 4.6.; and with lapack installed) generated a Makefile
that was flawless for the subsequent 'make'; and almost flawless for
the subsequent (sudo) 'make install'.

For that last one there were two lines with a minor issue:

1. MKDIR_P = @MKDIR_P@

had to change that into

MKDIR_P = /bin/mkdir -p


2. $(INSTALL) ./src/poy.1 $(DESTDIR)$(mandir)/poy.1

had to change that into

$(INSTALL) ./src/_build/poy.1 $(DESTDIR)$(mandir)/poy.1

(because 'make' generated poy.1 in the _build subdir of src, not in
src itself).



Apart from that, I reckon that you are aware of the compiler warnings
that get issued.



I also noticed that POY 5 still does not have a straightforward way to
deal with the problem that I pointed out in Cladistics 26: 453-455: I
have to apply the work-around to get correct results for Fig. 2. But
perhaps that is considered a feature :-).


Best

Jan
www.anagallis.be

On 2 jan, 21:43, Ward C Wheeler <whee...@amnh.org> wrote:
> POY users,
>
> We are please to announce the initial alpha release of POY5.  Many new features
> have been added  and others improved including maximum likelihood, chromosomal,
> and genomic analysis.

> [...]

[Nicholas Lucaroni]

Thanks for the bugfix information on the Makefile.

I am aware of the configuration warnings and there were plenty more a
few months ago. They've all come about in the new versions of gcc (4.5
and later). Currently I'm the only person on the team using gcc-4.6,
so they'll slowly get fixed.

-- Nick



On Jan 11, 2:30 pm, "jan.de.l...@skynet.be" <jan.de.l...@skynet.be>
wrote: