v4.0.4

Full Changelog: v4.0.3...v4.0.4

v4.0.3

fix #16

v4.0.2

• Portable string formatting with cinttypes.
• 32-bit architecture support.

v4.0.1

Fix error parsing stdin input
Updated robin-map and xxhash to newer versions, included them in the system libraries, and fixed CMakeLists

v4.0

Introduction of new thread levels for improved parallelization.
Enhanced performance through new parallel regions (e.g., ML Lengths, ML splits, LogLk, etc.).
Threads used in tree creation: Top hits, TopHitNJSearch, FastNJSearch, and ExhaustiveNJSearch (-slow).
Implementation of a faster tree partitioning approach with significant speed improvements.
Tree partitioning limited to NNI, SPR, and upProfiles computations for memory conservation:
Parallel tree traversal implemented for remaining parts.
Replacement of disk storage for profiles with Disk Computing.
Shared and reused Top upProfiles among threads for memory efficiency and accelerated sequential parts.
Improved non-deterministic mode with removal of mutex usage.
Optimized performance by parallelizing non-deterministic parts in deterministic mode:
Also implemented non-deterministic parts in deterministic mode for improved performance.
Deterministic mode now outperforms non-deterministic mode in terms of speed.
Tree partitioning method logging now hidden by default.
Support for Fastq format and libBZ2 compression.
Support for reading trees from NEXUS block trees.
Nvidia CUDA GPU computing support (experimental)
Introduced parallel compilation.
Incorporation of changes from FastTree-2.11.
Clang Support
Addressed critical errors and implemented substantial corrections.

v3.2.1

fix log inconsistency with multiple threads (only default verbose)

fix Segfault after memory update (issue 11)
fix other minor errors

v3.2.0

• v3.2.0:
  • Decrease in the peak memory usage.
  • Now profiles can be optionally stored on disk. It causes an important reduction in the memory usage.
  • All supported input files (NEXUS, Fasta and Phylip) can be used in compressed format (.zip and .gz)

v3.1.1

Maximum memory usage reduced, sequence is deleted when profile is cre…

…ated.

v3.1.0

-New tree partitioning algorithm
-Nexus format input support
-Thread mode argument for switching between deterministic and non-deterministic
-SPR steps parallel implementation
-Selected implementation info in the log
-Vector extensions have a different default value depending on the precision (-double-precision).

v3.0.1

-Bug fixes to errors reported by users
-Basic usage is now default GUI