Skip to content

@amkozlov amkozlov released this Mar 5, 2019 · 1 commit to master since this release

Optimizations and extensions

  • support model parameters in PAML format (--model PROTGTR{paml.txt}+G4)
  • TBE optimization (>100x faster thanks to @lutteropp)
  • safety checks can be disabled one-by-one, eg --force threads,.. or --force model_overfit
  • print trees on a (small) terrace into standard multi-line newick file
  • RF distance: accept multiple newick files separated by commas (eg. --rf tree1.nw,tree2.nw)
  • properly handle zero state frequencies via rate matrix reduction trick

Bugfixes

  • segfault in load balancing (rare special case)
  • fix empirical p-inv computation with pattern compression
  • #60: a rare bug in Brent optimization with values close to 0 (reported by @ephofmann)
  • --loglh: user-specified brlen scaler values were ignored

Minor

  • use 20 random starting trees by default if topological constraint is specified
  • --evaluate: save best-scoring tree into bestTree file
  • MPI: broadcast random seed
Assets 5
Pre-release
Pre-release

@amkozlov amkozlov released this Jan 11, 2019 · 20 commits to master since this release

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
Assets 5
Pre-release
Pre-release

@amkozlov amkozlov released this Oct 22, 2018 · 51 commits to master since this release

New features

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
Assets 5
Pre-release
Pre-release

@amkozlov amkozlov released this Jun 16, 2018 · 91 commits to master since this release

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
Assets 5
Pre-release
Pre-release

@amkozlov amkozlov released this Nov 28, 2017 · 173 commits to master since this release

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
Assets 5
Pre-release
Pre-release

@amkozlov amkozlov released this Sep 10, 2017 · 199 commits to master since this release

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
Assets 5
Pre-release
Pre-release

@amkozlov amkozlov released this Jul 25, 2017 · 211 commits to master since this release

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)
Assets 5
Pre-release
Pre-release

@amkozlov amkozlov released this Jun 1, 2017 · 217 commits to master since this release

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)
Assets 5
Pre-release
Pre-release

@amkozlov amkozlov released this Apr 26, 2017 · 227 commits to master since this release

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
Assets 5
Pre-release
Pre-release

@amkozlov amkozlov released this Apr 4, 2017 · 236 commits to master since this release

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
Assets 5
You can’t perform that action at this time.