PAL: Phylogenetic Analysis Library
PAL Release History
PAL was first publicly distributed in September 1999.
This and all subsequent releases can be downloaded by clicking
on the corresponding version number.
API Docs, or
- - A bit makeshift - lots of legacy code to deal with still, that's why it's just 1.5.1
- Substatial class rearrangement.
- Nexus alignment reading code (Alex Moore)
- Parially complete new maximum likelihood framework (will do very complex models - eventually).
- New Substitution Models and framework.
- New parameterized framework.
- New sample information framework.
- Temporal changes in substitution model.
- Probably a whole lot of otherthings...
|1.5 (src), or 1.5 (precompiled jar)
Substatial class rearrangement.
New alignment reading code.
Faster likelihood calculation.
ML tree searching for unrooted trees.
More comprehensive sUPGMA.
New src managment files (newmake.bat, and build.xml for ant).
New Codon Tables.
New tree rooting classes (with mid-point rooting).
Faster evolutionary distance calculation.
More Clustering methods.
Selection codon models (M1 and M2).
Tree label colouring, and font changing.
Two new packages, pal.popgen and pal.xml. Estimation of linkage disequilibrium.
Faster likelihood calculations. Improvement of tree classes and associated
functions. Many new helper functions. Classes dealing with XML.
Change of license from GPL to LGPL. Otherwise minor changes, e.g., updated
skyline plot class.
Codon models implemented (rate matrix, alignment, codon translation methods).
Utility functions for alignments (score function etc.). Splits, split systems
and corresponding tree distances (Robinson-Foulds). Extended utility
functions for trees (incl. Node factory). Pareto distribution. Classes for "measurably evolving
populations" (mep package). (April 2001).
Improvement of coalescent package: generalized skyline plot, new const.-to-exp.
growth demographic model, new features in IntervalsExtractor, new
classes DemographicTree/ClockTree. Reorganization of math and statistics
packages: new binomial, error and gamma functions in math package, and
bootstrap statistics (BIAS, VAR, CI etc), gamma, exponential, chi-square,
and normal distributions with pdf, cdf, and quantiles in statistics
package. New features in TreeUtils and NodeUtils, allowing for
a smaller SimpleTree class. SUPGMA tree reconstruction and distances.
Nucleotide-to-amino acid translation class. More GUI classes, e.g., for
circular trees. (December 2000).
Tree and Node classes turned into Interfaces implemented by SimpleNode and SimpleTree
and controlled by TreeUtils and NodeUtils classes.
New ParameterizedTree: Clock-trees with dated tips.
Much better accuracy and vast speed-ups in algorithm for
ML optimization of branch lengths for UnconstrainedTree, ClockTree, DatedTipsClockTree
(optimization delivers now "real-world" performance).
New tree comparison tests (e.g., Shimodaira-Hasegawa).
New protein models (VT, WAG, CPREV).
New classes for demographic models, coalescent simulation and coalescent priors.
Package names changed (clearer longer names), some classes reorganized, and two new packages
introduced (coalescent and util).
Macintosh compatibility (some file names changed). (July 2000).
Formation of PAL Development Core Team. PAL converted to pure library
(command applications moved into the Vanilla package). More efficient multivariate
minimization classes (non-linear conjugate gradient algorithms, line function
with boundaries, conjugate direction method with boundaries etc.) and improved
stop criteria. Automatic model selection among amino acids matrices. Inclusion
of the VT rate matrix. Estimation of model parameters without a tree. Several
smaller bug fixes and changes (alias mapping in Tree reversed plus subsequent
changes in TreeDistance and LikelihoodValue). (April 2000).
All classes are now fully documented using JavaDoc comments. Source
code complies to Java 1.0 language standard to allow compilation into native
code. Classes for evaluation of evolutionary hypotheses (chi-square and
likelihood computation) and interfaces for functions and of Parameterized
are reorganized. Detail improvements in a number of other classes. Introduction
of clock-constraint on trees. Some minor bug fixes. New platforms: direct
support for Windows and Unix-native (includes instructions for compilation
into native code using the GNU Compiler for Java). New applications: UPGMA
(constructs UPGMA tree), STRIPSITES (strips sites from an alignment according
to a given order). LSTREE and MLTREE now enable the estimation of clock-like
branch lengths. (February 2000).
Dog icon. Much improved classes for formatted input and output. PHYLIP
sequential format added. Restructuring of alignment package (e.g., removal
of TypedAlignment, changes in SitePattern, automatic data type detection).
Introduction of getInstance() methods in DataType and RateMatrix. Objects
for computing tree-induced distances and (weighted) squared distances between
distance matrices. Class for computing least-square branch length estimates.
CUI frontend now in a single common class for all CUI programs. New applications:
EVOLVE (generation of artificial data sets), LSTREE (least-squares estimates
of branch lengths), JUMBLE (randomizes sequence input order). (December
Complete reorganization of package layout and all classes. Main new
classes: ML evaluation of trees, estimation of model and branch parameters,
global optimization (genetic algorithm), likelihood ratio and Kishino-Hasegawa-Templeton
tests, random number generator, numerical derivatives of vectors. New application:
MLTREE (computation of likelihoods given a tree and estimation of model
parameters and branch lengths). Improvement of MLDIST program. (November1999).
||First public release. (September 1999).
||Project start. (January 1999).