RAxML-NG v0.8.0 BETA

IMPORTANT: New defaults

• 20 starting trees = 10 random + 10 parsimony (was: 1 random)
• scaled/proportional branch length model for partitioned alignments (was: linked)
• autoMRE bootstopping (was: 100 BS replicates)

New features

• Robinson-Foulds distance computation (--rfdist / --rf)
• print bootstrap replicate MSAs (--bsmsa)
• flexible MSA character maps for multistate data (see here)
• new AA substitution model: DEN (Kim 2018)

Bugfixes

• when using multiple starting trees, raxml.bestModel file used to store model params from the last tree search and not the one that yielded the best-scoring tree
• deadlock in --loglh with multiple threads
• fix CLV scaling with p-inv models (RAxML/ExaML seem to have this issue as well)
• duplicate taxon name check was broken since v0.7.0 (reported by Terry Jones)

Minor

• account for hyper-threading when detecting the number of CPU cores
• improve error messages for FASTA/PHYLIP formatting issues
• check if --prefix directory exists
• disable overfitting check for single-gene alignments

RAxML-NG v0.7.0 BETA

New features

• new support measure: Transfer Bootstrap Expectation (Lemoine et al., Nature 2018) : use --bs-metric tbe
• print AIC/AICc/BIC scores

Minor features and optimizations

• IMPORTANT: site repeats are now enabled by default (in case of problems: add --tip-inner on & please report!)
• improved load balancing: weight sites according to # states and # rate categories (in case of problems: add --extra lb-kassian & please report!)
• thread pinning by default in hybid MPI/pthread mode (--extra thread-nopin to disable)
• remove gap-only & duplicate sequences from the reduced alignment file
• build parsimony trees in master rank only
• check for invalid symbols (spaces,semicolons etc.) in taxon names (problems with Newick)

Bugfixes

• IMPORTANT: --support command was broken in v0.6.0, printing BS support values of 0
• improve base frequency normalization in empirical AA models (#46, thanks to @bredelings )
• increase precision of WAG rates (thanks to @bredelings )
• check for terraces only in --brlen unlinked mode
• fix model optimization with fixed branch lengths (--evaluate --opt-brances off)
• fully resolved/bifurcating constraint tree was ignored (reported by Lois Rancilhac)
• fix overflow in site repeats on very large unpartitioned alignments

RAxML-NG v0.6.0 BETA

New features

• support for binary (aka presence/absence) and multistate (aka morphological) models
• comprehensive and partial topological constraints (--tree-constraint)
• binary MSA format (a la ExaML)
• phylogenetic terrace detection using terraphast library (thanks to @upsj et al.)
• support for unlinked branch length mode in partitioned analyses (--brlen unlinked)
• automatic MRE-based bootstrap convergence check (also a posteriori with --bsconverge)
• outgroup rooting (--outgoup)

Minor features and optimizations

• separate command to generate starting trees (--start)
• (alias) command to compute tree loglh w/o optimization (--loglh)
• console-only mode (--nofiles)
• user-specified precision for logLH, branch length etc. (--precision)
• --parse command to compress alignment patterns, generate binary MSA and estimate resource requirements (RAM, #threads)
• random/parsimony/user starting trees can be combined in a single program invocation
• parsimony starting trees on mixed-datatype alignments
• faster restart from checkpoint by re-using existing starting trees and binary MSA file
• add missing SSE3 PLF kernels (major speedup on old pre-AVX machines)
• libll and pll-modules are now built with CMake (grand merci @BenoitMorel)

Bugfixes

• fix p-inv optimization in multi-threaded multi-partitioned runs (brent opt param broadcast)
• fix scaled branch length optimization when branches hit min/max value
• better error messages for ill-formatted partition files

RAxML-NG v0.5.1 BETA

This release contains multiple important bugfixes and several minor improvements.

BUGFIXES:

• fixed ML estimation of the proportion of invariant sites (+I)
• invalid bootstrap support values (>100) on datasets with 32N taxa (thanks to Shoyo Sato)
• fixed a bug in multi-partition parameter optimization involving LG4X/FreeRate models
• load balancing failed under very specific circumstances (thanks to Shoyo Sato)
• FreeRate model optimization failed when rates/weights approached the min/max values (thanks to Fabricia Ferreira Do Nascimento)
• fixed parallel reduction buffer overflow on alignments with 1000s of partitions
• several memory leaks in model parameter optimization routines

IMPROVEMENTS:

• new --check command: check alignment/partition file, remove all-gap columns (similar to -f c in RAxML8)
• PHYLIP parser is now ~10x faster on very long alignments (>10M sites, thanks to Mozes Blom)
• several improvements for short/small alignments (avoid full tree traversals, faster tip-tip lookup table pre-computation)
• parallelization hints: issue a warning if too few alignment patterns per thread are assigned
• add DNA model aliases to be compatible with ModelTest-NG

RAxML-NG v0.5.0 BETA

CRITICAL BUGFIX:

• bootstrap support values were consistently underestimated if and only if --all command was used with --bs-trees greater tha 250. Many thanks to Fabricia Nascimento for spotting and reporting this bug!

New features/enhancements:

• --support command: bootstrap mapping aka computing BS support values using an existing set of bootstrap trees from a newick file (similar to -f b option in old RAxML)
• site repeats optimization technique as described in (Kobert et al. 2016). This feature is still experimental and disabled by default; it can be enabled with --site-repeats on switch.
• faster AVX2 kernels for protein data (5%-20% speedup)
• automatically enable per-rate scalers on very large alignments (>2000 taxa) to prevent numerical underflow

RAxML-NG v0.4.1 BETA

Enhancements:

• better input validation and error reporting (alignment/starting tree)

Bugfixes:

• compilation with gcc7 (#17)
• failed assertion in MSA::remove_sites
• failed assertion in pllmod_algo_spr_round (fix libpll error propagation)
• fix excessive memory allocation during pattern compression (xflouris/libpll#143)

RAxML-NG v0.4.0 BETA

New features/enhancements:

• new PHYLIP parser (much faster, supports interleaved format)
• ascertainment bias correction
• median GAMMA rates

Bugfixes:

• fixed performance issue in tree evaluation mode
• fixed numerical issues with low alpha values (negative values in pmatrix, xflouris/libpll#125)

RAxML-NG v0.3.0 BETA

New features/enhancements:

• optimized model parameters are printed into $PREFIX.raxml.bestModel file
• better load balancing in bootstrapping

Bugfixes:

• pre-built binary now works on older CPUs without AVX support
• fixed memory leak in bootstrapping / multiple tree search mode
• existing log file was erroneously overwritten upon restart without the --redo option

RAxML-NG v0.2.0 BETA

This release fixes several bugs found in v0.1.0 and adds following new features:

• most model parameters (substitution rates, stationary frequencies, alpha etc.) can be set to user-defined values
• multiple user starting trees can be specified in a multi-line Newick file

RAxML-NG v0.1.0 BETA

First public release of the RAxML Next Generation.