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# Change Log
All notable changes to `libpll` will be documented in this file.
This project adheres to [Semantic Versioning](http://semver.org/).
## [0.3.2] - 2017-07-12
### Added
- Optional per-rate category scalers for protein and generic kernels
- Hardware detection for APPLE builds defaults to assembly code
### Fixed
- Improved fix for negative p-matrix values.
- Derivatives computation for Lewis/Felsenstein ascertainment bias correction
- set_tipchars() for ascertainment bias correction with non-DNA sequences
- Excessive memory allocation when compressing site patterns
- Issue with PHYLIP parsing when header ends with CRLF
## [0.3.1] - 2017-05-17
### Added
- Checks for older versions of clang and gcc to use assembly instructions
for cpu features detection
- Include guards for pll.h
### Fixed
- Correct updating of padded eigen-decomposition arrays for models with a
number of states not being a power of two
- Changed to the usage of builtin functions for cpu features detection
- Check for x86intrin.h
## [0.3.0] - 2017-05-15
### Added
- Run-time detection of cpu features
- Vectorized (AVX) computation of 20-state transition probability matrices
- Faster tip-inner kernels for 20-state models
- Improved AVX vectorization of derivatives
- Faster PHYLIP parser
- vectorized scaling for 20-state and arbitrary-state models
- AVX2 vectorizations for partials, likelihood and derivatives
- Unweighted parsimony functions including SSE, AVX and AVX2 vectorizations
- Randomized stepwise addition
- Portable functions for parsing trees from a C-string
- Optional per-rate category scalers to prevent numerical underflows on large
trees
- Setting of identity matrix if all exponentiations of eigenvalues multiplied
by branch length and rate are approximately equal to one
- Re-entrant cross-platform pseudo-random number generator
- Wrapper tree structures
- Custom exporting of tree structures using a callback function
- Support for median category rates in discrete gamma model
### Fixed
- Derivatives computation
- Parsing of branch lengths in newick trees
- Invariant sites computation
- Multiplication of log-likelihood with pattern weight after scaling term
- Added destructors for eliminating memory leaks when tree parsing fails
- Sumtable computation when having multiple substitution matrices
- Ascertainment bias computation
- Per-site log-likelihood computation
- Uninitialized values in testing framework
## [0.2.0] - 2016-09-09
### Added
- Methods for ascertainment bias correction (Lewis, Felsenstein, Stamatakis)
- Functions for performing NNI and SPR moves on unrooted trees
- Iterator function (pll_utree_every)
- Vectorized (AVX) computation of derivatives and sumtable
- restructure of source code such that higher-level functions call lower level
(core) functions
- Vectorized (AVX and SSE) functions for log-likelihood computation on rooted
and unrooted trees
- Implementation of Sankoff's dynamic programming parsimony algorithm, which
allows for arbitrary scoring matrices and facilitates ancestral state
reconstruction
- Faster vectorization scheme for computing partials under an arbitrary number
of states
- SSE vectorization for computing partials
- Faster lookup table constructionf or tip-tip case (PLL_ATTRIB_PATTERN_TIP)
- More error codes
- AVX and SSE vectorized functions for updating transition probability matrices
- SVG visualization for unrooted trees
- man pages
### Fixed
- When the number of states is not a power of 2, the log-likelihood results to
-inf if PLL_ATTRIB_PATTERN_TIP is used
- Missing memory initialization when using site pattern compression
- Erroneous charmap usage in pattern compression
- Removed likelihood computation from the function computing derivatives
- bug in unrooted tree clone function
## [0.1.0] - 2016-05-25
### Added
- AVX implementation for updating partials
- Core functions
- Selection between character states and cond. probability vectors for tips
- Compatibility with MS Windows
- Added basic PHYLIP parsing
- Functions for obtaining first/second derivatives to approximate LH function
- Trimming of line-feed/carriage-return when reading FASTA files
### Changed
- Selection of a specific rate matrix selection for each rate category
### Fixed
- Newick parsers handle arbitrary string literals as taxon names
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