What's new in POY 5.0.0 Beta
Aug 21, 2013
- New Features:
- report trees with branches would work for likelihood characters, but would
- not report parsimony branch lengths. The new command allows printing the
- branch lengths from three different methods (see below), these options are
- ignored under likelihood as we always report the parameter value that
- maximizes the log-likelihood.
- report graphtrees, asciitrees, and trees with collapsible property have
- been extended to use the branch lengths mentioned above (see command
- description below).
- Custom Alphabet transformation to static character via static approx. This
- was an issue with the characters that can be represented as prealigned and
- how to properly transform between them.
- Added support for ocaml PARMAP for generating fixed-state cost matrices.
- Added command report(robinson_foulds) (see command description below)
- Bugs Fixed:
- Selecting terminals caused an error in ncurses display when writing to an
- incorrect window (Louise Crowley).
- Transforming to likelihood under a model selection criteria (aic,aicc,bic)
- from a tcm under parsimony with different gap cost than substitution cost
- resulted (in failure) with added data that represents the cost of a gap.
- These should be filtered from the transformation, as in other likelihood
- transformations on those characters.
- Custom-alphabet implied alignment produced an alignment with extra indels.
- This was due to an encoding issue that became relevant when mixing custom
- alphabet characters and levels.
- Issue with missing data in custom-alphabet prealigned characters resolved.
- generation of cost-matrix with all-elements row/col and non-zero diagonal
- cost matrix --was being replaced with zeros, should have been min of row.
- No reported error when reading in sequence data with unequal fragments.
- This forced the computation to proceed as if those fragments were
- missing. Now (as in POY4) we report an error to the user.
- New Commands (see manual for full explanations) :
- report command for parsimony branch lengths
- report(trees:(branches:min))
- minimum number of changes is reported on branches
- report(trees:(branches:max))
- maximum number of changes is reported on branches
- report(trees:(branches:single))
- number of changes reported based on single assignment of dynamic
- characters
- report command for tree distances using Robinson Foulds distance metric
- report(robinson_foulds)
- will print matrix to terminal window
- report("OUTFILE", robinson_foulds)
- will print matrix to file OUTFILE
- Changed Commands (see manual for full explanations) :
- report command for collapsed branches has been changed. Instead of
- collapse:true or collapse:false, we've extended the command like the
- branch lengths above to collapse:min, collapse:max, collapse:single. The
- branch is collapsed when the length as defined above is equal to 0.0.
- report(trees:(collapse:single))
- report("tree.pdf", graphtrees:collapse:min)
- report( asciitrees:collapse:max )
New in POY 5.0.1 Alpha (Apr 6, 2012)
- 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.
New in POY 5.0.0 Alpha (Apr 6, 2012)
- 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]))
New in POY 4.1.2.1 (Nov 6, 2010)
- New Features:
- Added support for NEXUS output in the portal binary.
- Bugs Fixed:
- Output of NEXUS files when terminals are filtered, or dynamic homology characters are not present could produce errors or a file that POY itself could not read (Felipe G. Grazziotin).