POY 5.1 released
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Ward C Wheeler
Nov 1, 2013, 8:14:19 AM11/1/13
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POY users,
We are pleased to announce the release of POY 5.1. Several
new features and options
http://www.wiley.com/WileyCDA/WileyTitle/productCd-047067170X.html
have been added and others improved.
Perhaps the most important addition is the option "parallel" added to "swap()"
to allow the parallelization of swapping on individual trees. This will likely be most useful
for large, time consuming refinements such as under dynamic likelihood analysis.
Windows and OSX Binaries, source, and documentation are available at:
There is a known issue with the recently release OSX version 10.9 (Mavericks). We are encountering
seg faults which we are working to correct and will post when corrected.
Changes below.
As always, please contact us with bug reports and suggestions.
Enjoy,
The POY5 Team
CHANGES BETWEEN 5.0.0 and 5.1.0 Official Releases
New Features:
- Script Analyzer has some resolutions for parallel analysis that should
result in better performance of parallel execution.
- swap(parallel) command, see below.
- OPAM distribution via our github repo and basic_builder.sh. Please see our
opam-amnh repo (http://github.com/amnh/opam-amnh)
- Added initial level transformation of Aminoacid characters (during read);
previously we reported this option was being ignored.
Bugs Fixed:
- Reading morphology under Nexus had errors in processing SYMBOLS tag.
- Reading Nexus files with single quoted taxa-names failed.
- Parsering issue for trees with branch lengths in scientific notation and a
plus sign in their exponent, 1.0e+09. Now accept '+' symbol. (Thanks Cyrille)
- Under bremer (w/ negative constraints), nodes with excluded partitions were
not properly scored (as infinity); this resulted in trees with lower score
than expected during the bremer search.
- Correctly implemented the prealigned amino-acid characters to accept
resampling support techniques (jackkknife and bootstrap).
- Minor issues with basic_builder.sh with install and ./configure with parmap
- Certain level arguments were ignored since there are multiple ways to assign
level arguments, through the cost matrix assignment, or as an additional
argument (aminoacids and custom alphabet characters only).
- Fixed inlining C functions to support CLANG / OSX Mavericks.
New Commands (see manual for full explanations):
- Added documentation for commands in swap/build at_random, first, last. These
control how trees of the same cost are selected in the search/build. The
default is last, that is, the tree in memory is always replaced by the
newest found during a search/swap/build/fuse.
- swap(parallel) will swap in parallel a particular tree. This will allow
large trees that require a lot of computation (dynamic likelihood) to be
parallelized when a small number of trees are being analyzed. For example,
...
build(1)
transform(likelihood:(gtr,mpl,gap:coupled))
swap(parallel,all)
...
This will allow searching on the selected tree in parallel when the number
of nodes in the MPI run is > 1. The 'all' option is recommended so that each
node is fully utilized.
Known Issues :
- We have experienced segmentation faults on POY compiled on OSX 10.9
Mavericks with clang/LLVM3.3
New Features:
- Script Analyzer has some resolutions for parallel analysis that should
result in better performance of parallel execution.
- swap(parallel) command, see below.
- OPAM distribution via our github repo and basic_builder.sh. Please see our
opam-amnh repo (http://github.com/amnh/opam-amnh)
- Added initial level transformation of Aminoacid characters (during read);
previously we reported this option was being ignored.
Bugs Fixed:
- Reading morphology under Nexus had errors in processing SYMBOLS tag.
- Reading Nexus files with single quoted taxa-names failed.
- Parsering issue for trees with branch lengths in scientific notation and a
plus sign in their exponent, 1.0e+09. Now accept '+' symbol. (Thanks Cyrille)
- Under bremer (w/ negative constraints), nodes with excluded partitions were
not properly scored (as infinity); this resulted in trees with lower score
than expected during the bremer search.
- Correctly implemented the prealigned amino-acid characters to accept
resampling support techniques (jackkknife and bootstrap).
- Minor issues with basic_builder.sh with install and ./configure with parmap
- Certain level arguments were ignored since there are multiple ways to assign
level arguments, through the cost matrix assignment, or as an additional
argument (aminoacids and custom alphabet characters only).
- Fixed inlining C functions to support CLANG / OSX Mavericks.
New Commands (see manual for full explanations):
- Added documentation for commands in swap/build at_random, first, last. These
control how trees of the same cost are selected in the search/build. The
default is last, that is, the tree in memory is always replaced by the
newest found during a search/swap/build/fuse.
- swap(parallel) will swap in parallel a particular tree. This will allow
large trees that require a lot of computation (dynamic likelihood) to be
parallelized when a small number of trees are being analyzed. For example,
...
build(1)
transform(likelihood:(gtr,mpl,gap:coupled))
swap(parallel,all)
...
This will allow searching on the selected tree in parallel when the number
of nodes in the MPI run is > 1. The 'all' option is recommended so that each
node is fully utilized.
Known Issues :
- We have experienced segmentation faults on POY compiled on OSX 10.9
Mavericks with clang/LLVM3.3
Ward Wheeler
Division of Invertebrate Zoology
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024-5192
USA
http://www.wiley.com/WileyCDA/WileyTitle/productCd-047067170X.html
Cyrille D'Haese
Nov 4, 2013, 8:54:18 AM11/4/13
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When clicking "About POY", it writes "POY 5.0.0" and not 5.1...
Cyrille
Cyrille
Le 01/11/13 13:14, Ward C Wheeler a
écrit :
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-- Cyrille D'Haese UMR 7205 CNRS Origine, Structure et Evolution de la Biodiversite Departement Systematique et Evolution Museum National d'Histoire Naturelle CP50 - Entomologie 45 rue Buffon, 75231 Paris cedex 05, FRANCE Voice: +33 (0)1 40 79 57 36 Fax: +33 (0)1 40 79 56 79 e-mail: dha...@mnhn.fr
Nicholas Lucaroni
Nov 4, 2013, 11:27:46 AM11/4/13
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Thanks Cyrille, I seem to always forget to update that detail.
I've updated all the downloads to the changes provided by Cyrille and Gonzalo on the AMNH and Google Code sites.
I've updated all the downloads to the changes provided by Cyrille and Gonzalo on the AMNH and Google Code sites.
Regards,
Nicholas Lucaroni
POY Developer
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024
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