RAxML-NG v1.2.0

This release introduces multiple performance optimizations which yield 2x to 5x speedup for most typical analyses and datasets.

IMPORTANT: Due to change in defaults, the results are not compatible with previous raxml-ng versions. If you need to reproduce the behavior of raxml-ng 1.1.0 , add --extra compat-v11. Most changes can be also disabled one-by-one, please see instructions below:

New defaults & optimizations

• --search1: use parsimony starting tree by default
• bootstrap: use parsimony starting trees by default (add --extra bs-start-rand to use random starting trees as before)
• faster CLV updates in SPR rounds by @togkousa (#157), add --extra fastclv-off to disable
• new logLH epsilon defaults by @tschuelia: eps=1000 for brlen triplet optimization, eps=0.1 for final model optimization, eps=10 everywhere else (details: https://www.biorxiv.org/content/10.1101/2022.07.13.499893v1.full.pdf)
• parallelize parsimony starting tree computation (#151)

New features

• new amino-acid replacement matrices: Q.pfam, Q.bird, Q.insect, Q.mammal, Q.plant, Q.yeast (details: https://doi.org/10.1093/sysbio/syab010)
• arm64 support incl. vectorization via sse2neon library (#142)

Bugfixes

• fix regression failure with CATG input (#131)
• do not auto-enable rate scalers with >2000 taxa if --force / --force model_rate_scalers is specified (#133)
• partially incorrect TBE support values in --all mode
• --consense: fix error if result is a star tree (#143)
• invalid buffer size which led to failures in some parallel configurations (MPI with multiple workers per rank)
• truncate FASTA sequence names after the first space by default (#90). Alternatively, spaces can be converted to underscores with --msa-format fasta_longlabels.

Packaging note

This release is built with pll-modules 0.4.0, and libpll-2 0.4.0, and terraphast-0.1.0.