This file lists major changes between StatAlign releases. ------------------------------------------------------------------------------ StatAlign v3.4 on 12 Apr 2020 Bug fixes: * Removed restriction whereby only first five characters of PDB file name were used internally, causing issues for cases with multiple input files sharing the same first five characters ------------------------------------------------------------------------------ StatAlign v3.3 on 24 Oct 2018 New features: * MPI-based parallel version now available * Improvements to MCMC output files, to facilitate downstream analysis * Default is now to use branch-specific structural diffusivity parameters and B-factor-weighted baseline variance in command-line mode as well as with the GUI Bug fixes: * Removed static variable tempDoubleArray to avoid potential race condition * Bugfix to length=1 case in linearizerWeight * Errors in Utils.java now reported to STDERR rather than generating a popup window * Output PDB files now contain HIS instead of HSD * ModelExtension plugins now only contribute to the emission probability after the initial alignment has been generated ------------------------------------------------------------------------------ StatAlign v3.2 on 10 Feb 2015 New features: * Build process automated using Gradle * Consensus tree output includes percentage support for all internal nodes * Core model parameters printed to a separate log file * Minimum-risk summary alignment and column scores outputted to separate files Updates to StructAlign plugin (v1.1): * Analysis now possible for cases where not all sequences have known structure * Fix to spike mixture prior (relevant only to runs carried out using the 'sigmaSpike' option) * Fixed behaviour when stopping and restarting in GUI mode Bugfixes: * Fixed errors occuring in certain cases after removing sequences in GUI * Check for version update now works correctly * Plugin panels now no longer show in GUI when deactivated * Fixed issue where postprocessing files could be empty in RNA mode * Topology moves deactivated when only two sequences present ------------------------------------------------------------------------------ StatAlign v3.1 on 24 Nov 2013 New features: * Automatic proposal variance tuning for substitution parameters Updates to StructAlign plugin: * PDBReader for reading sequences and structures from a PDB file * B-factors and pairwise RMSD to annotate current alignment sample in GUI * Posterior probabilities shown above current alignment sample in GUI * Maximum likelihood structural superpositions are written to a PDB file Bugfixes: * Restored the toolbar icons of the postprocessing plugins * Fixed an issue that caused bias when sampling substitution parameters ------------------------------------------------------------------------------ StatAlign v3.0 on 26 Oct 2013 New features include: * StructAlign plugin for alignment of protein structures * Introduced framework for handling extensions to the evolutionary model * Significant improvements to mixing on tree topologies * Option to keep tree fixed when phylogeny is known * Several new types of MCMC moves to improve mixing and convergence * Automatic tuning for MCMC moves * Restructured code to allow for easy addition of new MCMC move objects * Code now allows for prior distributions to be easily specified * Selection of standard priors added (Gaussian, Gamma, etc.) Bugfixes: * Corrected an error that may have led to a small bias in the distribution of alignment proposal window lengths in certain cases * RNA mode now not activated for DNA sequences * Persistent regions of insertions with no descendants are stochastically removed using a new type of MCMC move ------------------------------------------------------------------------------ StatAlign v2.1 on 24 Feb 2013 Improvements: * GUI update: launching an analysis requires less clicks * New welcome message and About box * Output files are summarised after the analysis Bugfixes: * RNA mode automatically disabled for non-RNA input in console mode * Plugins that do not produce output will not create files * Fix to allow the RNAalifold plugin to run in console mode as well * Removed error message for input files that don't end in .fas(ta) * PPFold fix for non-UK/US locales * Fixed long-standing bug in Tamura-Nei model ------------------------------------------------------------------------------ StatAlign v2.0 on 28 Sep 2012 New features: * Integration of RNA secondary structure prediction tools (PPfold and RNAalifold) and consensus structure calculation * RNA visualisation with VARNA * Automation of MCMC parameter setup * Consensus tree and network plugins with visualisation * Metropolis-coupled MCMC with parallelisation (currently unavailable) * GUI update including toolbar and buttons Improvements and bugfixes: * New command line options * Postprocessing API revised * Postprocessing output defaults changed * Fixed a bug in GTR model that caused StatAlign to freeze in some cases - we thank William Majoros for reporting and providing a fix * Fixed a bug that caused U characters in RNA sequences to be removed ------------------------------------------------------------------------------ StatAlign v1.21a on 14 July 2011 New features: * Ambiguous nucleotide/amino acid support Improvements and bugfixes: * Improved command line interface * Output files are named automatically * Alignment visualisation revised * Postprocessing panel updates improved * Various minor fixes and additions ------------------------------------------------------------------------------ StatAlign v1.1 on 18 July 2008 New features: * Basic command line interface added Improvements: * Various minor fixes ------------------------------------------------------------------------------ StatAlign v1.0 in June 2008 The initial StatAlign release.