libpll 0.3.0

Changes

• 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
• Fixed parsing of branch lengths in newick trees
• Fixed computation of invariant sites
• Multiplication of log-likelihood with pattern weight after scaling term
• Added destructors for eliminating memory leaks when tree parsing fails
• Fixed sumtable computation when having multiple substitution matrices
• Fixed ascertainment bias computation
• Fixed per-site log-likelihood computation
• Fixed uninitialized values in testing framework

Notes

1. The file libpll-0.2.0-linux-x86_64.tar.gz is a pre-compiled binary of libpll.
2. The file libpll-src-0.3.0.tar.gz contains the libpll source code and does not require autotools installed.
3. Files v0.3.0.tar.gz and 0.3.0.zip are generated by GitHub, and require autotools installed (as when cloning the repository).