What's Changed
- Update new ModelFinder multi-threading strategy by @HuaiyanRen in #180
- Bug fixes AliSim: buffer overflow and very short branches/partitions by @trongnhanuit in #185
- Merge PR #185 by @HuaiyanRen in #188
- Bug fix: stop using dangling ptrs and buildPattern() in fixPartitions() by @StefanFlaumberg in #186
- PartitionFinder-mAIC improvement by @HuaiyanRen in #202
- Fix AliSim crashing when using GHOST with a partitioned/mixed-datatype models by @trongnhanuit in #191
- Bug fix: uniformly select indel positions across only non-gap sites by @trongnhanuit in #197
- Mutsel implementation by @benjamin-lieser in #193
- Error out when a partition model is combined with -fs/-ft instead of silently ignoring them by @ssolo in #208
- Fix setRootNode() assertion when the -o outgroup is absent from a partition tree or a quartet tree (#203, #89) by @cindykrafft in #207
- Use different memory thresholds for different platforms in ci workflow by @thomaskf in #209
- use different thresholds for different platforms in time testing by @thomaskf in #212
- Fix MutSel potential bugs related to alignment copying by @StefanFlaumberg in #211
- Honour user-defined codon frequencies (+FU) for GY-type models by @cindykrafft in #210
- Fix the CI workflow by @thomaskf in #213
- Mixlen refactoring: Remove dependency on ModelFactoryMixlen and cppoptlib, add support for the -ft option by @StefanFlaumberg in #182
- Remove -ft AUTO and match benchmark thresholds by identifier by @thomaskf in #215
New Contributors
- @benjamin-lieser made their first contribution in #193
- @ssolo made their first contribution in #208
- @cindykrafft made their first contribution in #207
Full Changelog: v3.1.3...v3.1.4
Contributors
ssolo, trongnhanuit, and 5 other contributors