hyphy - 2.5.79

What's Changed

• Add GitHub Action to automatically update Homebrew formula by @stevenweaver in https://github.com/veg/hyphy/pull/1895
• 2.5.79 by @spond in https://github.com/veg/hyphy/pull/1896

Full Changelog: https://github.com/veg/hyphy/compare/2.5.78...2.5.79

- HyPhy
Published by spond 6 months ago

hyphy - 2.5.78

What's Changed

• Fix build on i386 (32-bit x86) by @Jehops in https://github.com/veg/hyphy/pull/1892
• 2.5.78 by @spond in https://github.com/veg/hyphy/pull/1894

Full Changelog: https://github.com/veg/hyphy/compare/2.5.77...2.5.78

- HyPhy
Published by spond 6 months ago

hyphy - 2.5.77

What's Changed

• 2.5.77 by @spond in https://github.com/veg/hyphy/pull/1891

Full Changelog: https://github.com/veg/hyphy/compare/2.5.76...2.5.77

- HyPhy
Published by spond 6 months ago

hyphy - 2.5.76

What's Changed

• Develop catchup with master by @spond in https://github.com/veg/hyphy/pull/1872
• Code cleanup and refactoring. by @spond in https://github.com/veg/hyphy/pull/1881
• Feature/modernize cmake by @spond in https://github.com/veg/hyphy/pull/1874
• GCC 9 minimum by @spond in https://github.com/veg/hyphy/pull/1882
• Trying to solve an odd compilation issue on silverback by @spond in https://github.com/veg/hyphy/pull/1883
• Fixes by @spond in https://github.com/veg/hyphy/pull/1884
• Fixing CMake options for WASM by @spond in https://github.com/veg/hyphy/pull/1885
• 2.5.76 by @spond in https://github.com/veg/hyphy/pull/1886

Full Changelog: https://github.com/veg/hyphy/compare/2.5.75...2.5.76

- HyPhy
Published by spond 6 months ago

hyphy - 2.5.75

What's Changed

• 2.5.75 by @spond in https://github.com/veg/hyphy/pull/1871

Full Changelog: https://github.com/veg/hyphy/compare/2.5.74...2.5.75

- HyPhy
Published by spond 7 months ago

hyphy - 2.5.74

What's Changed

• Add MSS Codon GA support by @hverdonk in https://github.com/veg/hyphy/pull/1863
• 2.5.74 by @spond in https://github.com/veg/hyphy/pull/1866 Full Changelog: https://github.com/veg/hyphy/compare/2.5.73...2.5.74

- HyPhy
Published by spond 8 months ago

hyphy - 2.5.73

What's Changed

• adding CTestTestfile.cmake to gitignore list by @stevenweaver in https://github.com/veg/hyphy/pull/1855
• Adding BUSTED-PH; some other improvements and bug fixes by @spond in https://github.com/veg/hyphy/pull/1856 Full Changelog: https://github.com/veg/hyphy/compare/2.5.72...2.5.73

- HyPhy
Published by spond 10 months ago

hyphy - 2.5.72

What's Changed

• Add WebAssembly build GitHub Action by @stevenweaver in https://github.com/veg/hyphy/pull/1845
• sync with master branch by @stevenweaver in https://github.com/veg/hyphy/pull/1846
• Remove benchmarks workflow and related files by @stevenweaver in https://github.com/veg/hyphy/pull/1847
• master sync by @stevenweaver in https://github.com/veg/hyphy/pull/1848
• Remove all references to DoSQL functionality by @stevenweaver in https://github.com/veg/hyphy/pull/1844
• Adding duplicate sequence remover to standard analyses by @hverdonk in https://github.com/veg/hyphy/pull/1841
• 2.5.72 by @spond in https://github.com/veg/hyphy/pull/1850
• Fix BGM error
• Fix PRIME propetry error
• Improve help message generation
• Fix !( parsing error

Full Changelog: https://github.com/veg/hyphy/compare/2.5.70...2.5.72

- HyPhy
Published by spond 10 months ago

hyphy - 2.5.71

What's Changed

• BUSTED+MSS.
• Minor bug fixes by @spond in https://github.com/veg/hyphy/pull/1823
• Molerate Full Changelog: https://github.com/veg/hyphy/compare/2.5.69...2.5.71

- HyPhy
Published by spond 11 months ago

hyphy - 2.5.70

What's Changed

• BUSTED+MSS. Minor bug fixes by @spond in https://github.com/veg/hyphy/pull/1823

Full Changelog: https://github.com/veg/hyphy/compare/2.5.69...2.5.70

- HyPhy
Published by spond 11 months ago

hyphy - 2.5.69

What's Changed

• 2.5.68 by @spond in https://github.com/veg/hyphy/pull/1801

Full Changelog: https://github.com/veg/hyphy/compare/2.5.67...2.5.69

What's Changed

• Develop by @spond in https://github.com/veg/hyphy/pull/1815

Full Changelog: https://github.com/veg/hyphy/compare/2.5.68...2.5.69

- HyPhy
Published by spond 12 months ago

hyphy - 2.5.68

What's Changed

• 2.5.68 by @spond in https://github.com/veg/hyphy/pull/1801

Full Changelog: https://github.com/veg/hyphy/compare/2.5.67...2.5.68

- HyPhy
Published by spond about 1 year ago

hyphy - 2.5.67

What's Changed

• 2.5.67 by @spond in https://github.com/veg/hyphy/pull/1798

Full Changelog: https://github.com/veg/hyphy/compare/2.5.66...2.5.67

- HyPhy
Published by spond about 1 year ago

hyphy - 2.5.66

What's Changed

• 2.6.65 by @spond in https://github.com/veg/hyphy/pull/1778
• add dockerfile by @d-callan in https://github.com/veg/hyphy/pull/1784
• 2.5.66 RC by @spond in https://github.com/veg/hyphy/pull/1795

New Contributors

• @d-callan made their first contribution in https://github.com/veg/hyphy/pull/1784

Full Changelog: https://github.com/veg/hyphy/compare/2.5.64...2.5.66

- HyPhy
Published by spond about 1 year ago

hyphy - 2.5.65

What's Changed

• 2.6.65 by @spond in https://github.com/veg/hyphy/pull/1778

Full Changelog: https://github.com/veg/hyphy/compare/2.5.64...2.5.65.actual

- HyPhy
Published by spond about 1 year ago

hyphy - 2.5.64

Minor bug fixes.

- HyPhy
Published by spond about 1 year ago

hyphy - 2.5.63

What's Changed

• doc: Add -c bioconda to conda install by @corneliusroemer in https://github.com/veg/hyphy/pull/1729
• doc: Make build instructions less confusing by @corneliusroemer in https://github.com/veg/hyphy/pull/1732
• 2.5.63 by @spond in https://github.com/veg/hyphy/pull/1750

New Contributors

• @corneliusroemer made their first contribution in https://github.com/veg/hyphy/pull/1729

Full Changelog: https://github.com/veg/hyphy/compare/2.5.62...2.5.63

- HyPhy
Published by spond over 1 year ago

hyphy - 2.5.62

Bug fixes and improvements.

- HyPhy
Published by spond over 1 year ago

hyphy - 2.5.61

Bug fixes, minor enchancements.

- HyPhy
Published by spond almost 2 years ago

hyphy - 2.5.60

What's Changed

• 2.5.60 RC by @stevenweaver in https://github.com/veg/hyphy/pull/1695

Full Changelog: https://github.com/veg/hyphy/compare/2.5.59...2.5.60

- HyPhy
Published by stevenweaver almost 2 years ago

hyphy - 2.5.59

What's Changed

• Develop by @spond in https://github.com/veg/hyphy/pull/1677

Full Changelog: https://github.com/veg/hyphy/compare/2.5.58...2.5.59

- HyPhy
Published by stevenweaver about 2 years ago

hyphy - 2.5.59

-- Speed improvements -- More agressive optimization settings -- Faster evaluation of "expensive" formulas in transition matrices -- Bug fixes in MEME and a few other tweaks here and there.

- HyPhy
Published by spond about 2 years ago

hyphy - 2.5.58

1. aBSREL 2.5
2. BUSTED+E
3. RELAX diagnostic reports
4. ZLIB compressed output via GZIP_OUTPUT=TRUE; env
5. Bug fixes.

- HyPhy
Published by spond about 2 years ago

hyphy - 2.5.57

What's Changed

• increased max number of GA rate classes from 5 to 6 by @hverdonk in https://github.com/veg/hyphy/pull/1649
• remove debug flags from production targets by @stevenweaver in https://github.com/veg/hyphy/pull/1665

New Contributors

• @hverdonk made their first contribution in https://github.com/veg/hyphy/pull/1649

Full Changelog: https://github.com/veg/hyphy/compare/2.5.56...2.5.57

- HyPhy
Published by stevenweaver over 2 years ago

hyphy - 2.5.56

What's Changed

• BIOWASM support
• 2.5.56 by @stevenweaver in https://github.com/veg/hyphy/pull/1664

Full Changelog: https://github.com/veg/hyphy/compare/2.5.55...2.5.56

- HyPhy
Published by stevenweaver over 2 years ago

hyphy - 2.5.55

Bug fixes, minior optimizations, and analysis updates.

-- MEME to v4 : support for MH, imputation, and >2 rate classes -- BUSTED to v4.5 : support for error-sink -- aBSREL bug fixes.

- HyPhy
Published by spond over 2 years ago

hyphy - 2.5.53

What's Changed

• emscripten support by @stevenweaver in https://github.com/veg/hyphy/pull/1642

Full Changelog: https://github.com/veg/hyphy/compare/2.5.52...2.5.53

- HyPhy
Published by stevenweaver over 2 years ago

hyphy - v2.5.52

-- Bug fixes and improvements -- Improved FEL and MEME stability -- Added support for multiple hits to FEL

- HyPhy
Published by spond over 2 years ago

hyphy - 2.5.51

Bug fixes.

Should remove some internal numerical errors Memory leaks fixed Updated compilation for SWIG Updated setup.py in src/lib along with various examples.

- HyPhy
Published by spond over 2 years ago

hyphy - 2.5.50

Full Changelog: https://github.com/veg/hyphy/compare/2.5.49...2.5.50

- HyPhy
Published by stevenweaver almost 3 years ago

hyphy - 2.5.49

-- ARM NEON fix for likelihood scaling -- Added features to HBL commands and minor enhancements

- HyPhy
Published by spond almost 3 years ago

hyphy - 2.5.48

Bug fixes, minor enhancements, and some new features.

- HyPhy
Published by spond almost 3 years ago

hyphy - 2.5.47

Code refactoring and some speed improvements.

1. Redid product-sum code for the pruning algorithm to use cache-aware blocking and better use of SIMD.
2. Improved likelihood calculation speed for some models by caching how parameter changes are propagated to tree nodes.
3. Bug fixes.

- HyPhy
Published by spond about 3 years ago

hyphy - 2.5.46

1. Re-released with a hotfix for issue #1555
2. Speed improvements.
3. Restored auto-benchmarking under OpenMP
4. Fixed an issue with computing the likelihood function when an internal node is fixed at a given character (affected was, among other things, marginal ancestral state reconstruction)

- HyPhy
Published by spond about 3 years ago

hyphy - 2.5.45

Across the board 10-40% speed ups for core functions (esp codon models).

- HyPhy
Published by spond about 3 years ago

hyphy - 2.5.43

Bug fixes, minor feature additions.

- HyPhy
Published by spond about 3 years ago

hyphy - 2.5.42

-- Bug fixes, including internal errors on certain multi-partition optimization -- Minor fixes to lib and code cleanup

- HyPhy
Published by spond over 3 years ago

hyphy - 2.5.41

-- Fix several RELAX.bf issues -- Fix build issues when no OpenMP is present

- HyPhy
Published by spond over 3 years ago

hyphy - 2.5.40

Bug fixes and analysis enhancements

- HyPhy
Published by spond over 3 years ago

hyphy - 2.5.39

-- Optimization for BS-REL models -- Bug and memory leak fixes -- BUSTED v4.0

- HyPhy
Published by spond over 3 years ago

hyphy - 2.5.38

Bug fixes, analysis enhancements.

- HyPhy
Published by spond almost 4 years ago

hyphy - 2.5.36

Bug fixes. Analysis enhancements. SRV support for aSBREL.

- HyPhy
Published by spond about 4 years ago

hyphy - 2.5.33

FEL and MEME bootstrap support. Minor bug fixes.

- HyPhy
Published by spond over 4 years ago

hyphy - 2.5.32

Method enhancement and bug fixes.

- HyPhy
Published by spond over 4 years ago

hyphy - 2.5.31

-- Bug fixes -- Adding support for ZLIB. You can now specify .gz compressed files as --alignment arguments.

- HyPhy
Published by spond almost 5 years ago

hyphy - 2.5.30

Minor bug fixes and enhancements.

- HyPhy
Published by spond almost 5 years ago

hyphy - 2.5.29

GARD improvements. Multiple bug fixes.

- HyPhy
Published by spond almost 5 years ago

hyphy - 2.5.28

Minor bug fixes. MSS model.

- HyPhy
Published by spond about 5 years ago

hyphy - 2.5.27

Adding --full-model No to FEL and MEME. Bug fixes. Minor improvements.

- HyPhy
Published by spond about 5 years ago

hyphy - 2.5.26

Bug fixes relating to constraint violations in RELAX (was broader than that). Added the --precision option to FEL to allow more rapid data fitting at the expense of less precise optimization.

- HyPhy
Published by spond about 5 years ago

hyphy - 2.5.25

Bug fixes and speed improvements.

- HyPhy
Published by spond about 5 years ago

hyphy - 2.5.24

Adds support for ARM NEON (Apple M1). Bug fixes and improvements.

- HyPhy
Published by spond about 5 years ago

hyphy - 2.5.23

Bug fixes

- HyPhy
Published by spond over 5 years ago

hyphy - 2.5.22

- HyPhy
Published by spond over 5 years ago

hyphy - 2.5.21

- HyPhy
Published by spond over 5 years ago

hyphy - 2.5.20

Bug fixes, speed improvements.

- HyPhy
Published by spond over 5 years ago

hyphy - 2.5.19

v2.5.19; focused on performance improvements, codebase cleanup, and bug fixes.

- HyPhy
Published by spond over 5 years ago

hyphy - 2.5.18

Fixing compilation error when NOAVX is enabled

- HyPhy
Published by spond over 5 years ago

hyphy - 2.5.17

Fixes issues introduced in 2.5.16; better scaling for larger datasets; optimization boundary cases fixes. Addresses most of issue 1190.

- HyPhy
Published by spond over 5 years ago

hyphy - 2.5.16

Speedups, bug fixes, some HBL libv3 improvements.

- HyPhy
Published by spond over 5 years ago

hyphy - 2.5.15

Bug fixes, optimization improvements, code cleanup.

- HyPhy
Published by spond over 5 years ago

hyphy - 2.5.14

Minor bug fixes; changing most site-level optimizations to use nedler-mead and more extensive init grid; move lib to share

- HyPhy
Published by spond almost 6 years ago

hyphy - 2.5.12

Several important optimizer fixes and improvements. Fixes for HMM models. Add HMM option in SRV to BUSTED[S]

- HyPhy
Published by spond almost 6 years ago

hyphy - 2.5.11

Bug fixes and speed improvements.

- HyPhy
Published by spond almost 6 years ago

hyphy - 2.5.10

Bug fix (soft errors) where automatically renamed sequence names would not be reflected in the corresponding topology

- HyPhy
Published by spond almost 6 years ago

hyphy - 2.5.9

Bug fixes and improvements added MH support for aBSREL added state imputation for PRIME zero-branch length squashing for standard selection analyses

- HyPhy
Published by spond almost 6 years ago

hyphy - 2.5.8

Adding PRIME, minor enchacements

- HyPhy
Published by spond almost 6 years ago

hyphy - 2.5.7

-- Fixing pesky optimizer boundary cases -- Fixing a serious memory bloat issue in MPI-enabled analyses, esp GARD -- Basic Iterators in HBL -- Improvements to some optimization settings

- HyPhy
Published by spond almost 6 years ago

hyphy - 2.5.6

Better testing, fixes for bugs in MEME and RELAX in 2.5.5

- HyPhy
Published by spond almost 6 years ago

hyphy - 2.5.5

THIS RELEASE IS BUGGY

Do not use for MEME AND RELAX analyses.

- HyPhy
Published by spond almost 6 years ago

hyphy - 2.5.4

GARD fixes.

- HyPhy
Published by spond about 6 years ago

hyphy - 2.5.3

GARD issue hot fix, prevent crash that could occur during error handling

- HyPhy
Published by spond about 6 years ago

hyphy - 2.5.2

Incremental bug fixes, analysis updates.

- HyPhy
Published by spond about 6 years ago

hyphy - 2.5.1

• Allows -DNOAVX=ON rule to work with Clang

- HyPhy
Published by stevenweaver over 6 years ago

hyphy - 2.5.0

Notable Changes: Far to many to list here in detail but to name a few... - Completely re-engineered computational core and analysis library - New classes of evolutionary models and statistical tests - Dramatic performance and stability enhancements - Significant usability improvements including command line arguments and relative paths

Stay tuned for a release note describing the redesign in detail.

- HyPhy
Published by rdvelazquez over 6 years ago

hyphy - 2.4.0-alpha.2

SM-2019 update for Galaxy. Still under active development and not fully ready for use.

- HyPhy
Published by rdvelazquez almost 7 years ago

hyphy - 2.4.0-alpha.1

Still under active development and not fully ready for use.

- HyPhy
Published by stevenweaver about 7 years ago

hyphy - 2.3.14

Notable Changes

• BGM has been ported to use libv3 library.

Issues Addressed in this Release

• #820 - Problem accessing BGM/Spidermonkey from command line
• #817
• #809

Please see the associated pull request for a complete listing of commits included in this release.

- HyPhy
Published by stevenweaver over 7 years ago

hyphy - 2.3.13

Notable Changes

Please see the associated pull request for a complete listing of commits included in this release.

- HyPhy
Published by stevenweaver almost 8 years ago

hyphy - 2.3.12

Notable Changes

• Bug fixes for #789 - Fixes compilation issue on FreeBSD

Please see associated pull request and pull request for a complete listing of commits included in this release.

- HyPhy
Published by stevenweaver almost 8 years ago

hyphy - 2.3.11

Notable Changes

• Bug fixes for #743, #746, and #748

Please see the associated pull request for a complete listing of commits included in this release.

- HyPhy
Published by stevenweaver about 8 years ago

hyphy - 2.3.10

Notable Changes

• Bug fix for #738 (Stephen Shank)

Please see the associated pull request for a complete listing of commits included in this release.

- HyPhy
Published by stevenweaver about 8 years ago

hyphy - 2.3.9

Notable Changes

• Bug fixes for #709 and #723 (Sergei Pond and Stephen Shank)

Please see the associated pull request for a complete listing of commits included in this release.

- HyPhy
Published by stevenweaver about 8 years ago

hyphy - 2.3.8

Notable Changes

• LEISR 0.4 (Stephanie Spielman and Sergei Pond)
• Bug fixes for #703 and #712 (Sergei Pond and Steven Weaver)

Please see the associated pull request for a complete listing of commits included in this release.

- HyPhy
Published by stevenweaver about 8 years ago

hyphy - 2.3.7

Notable Changes

• [#696] Five new amino acid models (Stephanie Spielman)

  • "mtMAM" - "Empirical model of protein evolution for mammalian mitochondrial genomes from Yang N, Nielsen R, and Hasegawa M. (1998). Ref: http://dx.doi.org/10.1093/oxfordjournals.molbev.a025888,
  • "cpREV" - "Empirical model of protein evolution for chloroplast genomes from from Adachi et al. (2000). Ref: https://www.ncbi.nlm.nih.gov/pubmed/10795826"
  • "HIVBm" - "Empirical model of protein evolution for between-host HIV sequences from Nickle et al. (2007). Ref: https://doi.org/10.1371/journal.pone.0000503"
  • "HIVWm" - "Empirical model of protein evolution for within-host HIV sequences from Nickle et al. (2007). Ref: https://doi.org/10.1371/journal.pone.0000503"
  • "AB" - "Empirical model of protein evolution for antibody sequences from Mirsky et al. (2015). Ref: https://doi.org/10.1093/molbev/msu340"

• [#683] GARD results formatted to be consistent with other methods (Steven Weaver)

• Bug fixes for #685, #687, #689, and #700 (Sergei Pond)

Please see the associated pull request for a complete listing of commits included in this release.

- HyPhy
Published by stevenweaver over 8 years ago

hyphy - 2.3.6

Notable Changes

• Includes LEISR - Likelihood Estimation of Individual Site Rates (Stephanie Spielman)
• Bug fixes

Please see the associated pull request for a complete listing of commits included in this release.

- HyPhy
Published by stevenweaver over 8 years ago

hyphy - 2.3.4

Notable Changes

• [e2301c6] A new binary model has been added in libv3 (Stephanie Spielman)
• [e8c365e] A new DNA model (JC69) (Stephanie Spielman)

Other changes include additional tests and bug fixes to HBL. Please see #623 for a complete listing of commits included in this release.

- HyPhy
Published by stevenweaver over 8 years ago

hyphy - 2.3.5

Notable Changes

• Xcode 9 compatibility

Addresses issue where LLVM 4.0 (which is part of Xcode 9) throws a fatal error for ordered comparison between pointer and zero.

- HyPhy
Published by stevenweaver over 8 years ago

hyphy - 2.3.3

• FUBAR migration to new library
• bug fixes

- HyPhy
Published by stevenweaver over 8 years ago

hyphy - 2.3.2

• Fixes tree iteration bug exposed by FLEA
• Includes aBSREL unit test
• Build integration improvements

- HyPhy
Published by stevenweaver over 8 years ago

hyphy - 2.3.1

- HyPhy
Published by stevenweaver over 8 years ago

hyphy - 2.3.0

This is a reasonable recent version which could be used to support HBL written in 2016-2017

- HyPhy
Published by spond over 8 years ago

hyphy - 2.2.7

• GCC 6 compatibility
• Fixes version recognition in BUSTED batch file
• Adds RELAX to list of Standard Analyses in GUI

- HyPhy
Published by stevenweaver over 9 years ago

hyphy - 2.3.0-alpha

- HyPhy
Published by stevenweaver over 10 years ago

hyphy - 2.2.6

bug fixes

- HyPhy
Published by spond over 10 years ago

hyphy - 2.2.5

Updates licensing.

- HyPhy
Published by stevenweaver over 10 years ago

hyphy - 2.2.4

Bug fixes, analysis updates

- HyPhy
Published by spond almost 11 years ago

hyphy - 2.2.3

Bug fixes, new analyses.

- HyPhy
Published by spond about 11 years ago

hyphy - 2.2.2

Bug fixes and minor feature additions.

- HyPhy
Published by spond over 11 years ago

hyphy - 2.2.1

Cumulative 2013-2014 bug fixes and improved analysis modules.

- HyPhy
Published by stevenweaver over 11 years ago