examl - Exascale Maximum Likelihood (ExaML) code for phylogenetic
inference examl-AVX - Exascale Maximum Likelihood (ExaML) code for
phylogenetic inference using AVX examl-OMP - Exascale Maximum Likelihood
(ExaML) code for phylogenetic inference using OMP examl-OMP-AVX - Exascale
Maximum Likelihood (ExaML) code for phylogenetic inference using AVX and
OMP
examl|examl-AVX|examl-OMP|examl-OMP-AVX -s
binarySequenceFileName -n outputFileNames -m
rateHeterogeneityModel -t userStartingTree|-R binaryCheckpointFile|-g
constraintTree -p randomNumberSeed [-np NP] [-a] [-B
numberOfMLtreesToSave] [-c numberOfCategories] [-D] [-e likelihoodEpsilon]
[-f d|e|E|o|q] [-h] [-i initialRearrangementSetting] [-I
quartetCheckpointInterval] [-M] [-r randomQuartetNumber] [-S] [-v] [-w
outputDirectory] [-Y quartetGroupingFileName]
[--auto-prot=ml|bic|aic|aicc]
- -np NP
- NP is the number of processors to use for MPI. If not specified some
hopefully sensible guess is made. This is a specific option of the
Debian wrapper in /usr/bin.
- -a
- use the median for the discrete approximation of the GAMMA model of rate
heterogeneity
- DEFAULT: OFF
- -B
- specify the number of best ML trees to save and print to file
- -c
- Specify number of distinct rate catgories for ExaML when modelOfEvolution
is set to GTRPSR Individual per-site rates are categorized into
numberOfCategories rate categories to accelerate computations.
- DEFAULT: 25
- -D
- ML search convergence criterion. This will break off ML searches if the
relative Robinson-Foulds distance between the trees obtained from two
consecutive lazy SPR cycles is smaller or equal to 1%. Usage recommended
for very large datasets in terms of taxa. On trees with more than 500 taxa
this will yield execution time improvements of approximately 50% While
yielding only slightly worse trees.
- DEFAULT: OFF
- -e
- set model optimization precision in log likelihood units for final
optimization of model parameters
- DEFAULT: 0.1
- -f
- select algorithm:
- "-f d": new rapid hill-climbing
- DEFAULT: ON
- "-f e": compute the likelihood of a bunch of trees passed via
-t
- this option will do a quick and dirty optimization without re-optimizng
the model parameters for each tree
- "-f E": compute the likelihood of a bunch of trees passed via
-t
- this option will do a thorough optimization that re-optimizes the model
parameters for each tree
- "-f o": old and slower rapid hill-climbing without heuristic
cutoff
- "-f q": fast quartet calculator
- DEFAULT for "-f": new rapid hill climbing
- -g
- Pass a multi-furcating constraint tree to ExaML. The tree needs to contain
all taxa of the alignment! When using this option you also need to specify
a random number seed via "-p"
- -h
- Display this help message.
- -i
- Initial rearrangement setting for the subsequent application of
topological changes phase
- -I
- Set after how many quartet evaluations a new checkpoint will be
printed.
- DEFAULT: 1000
- -m
- Model of rate heterogeneity
- select "-m PSR" for the per-site rate category model (this used
to be called CAT in RAxML) select "-m GAMMA" for the gamma model
of rate heterogeneity with 4 discrete rates
- -M
- Switch on estimation of individual per-partition branch lengths. Only has
effect when used in combination with "-q" Branch lengths for
individual partitions will be printed to separate files A weighted average
of the branch lengths is computed by using the respective partition
lengths
- DEFAULT: OFF
- -n
- Specifies the name of the output file.
- -p
- Specify a random number seed, required in conjunction with the
"-g" option for constraint trees
- -R
- read in a binary checkpoint file called
ExaML_binaryCheckpoint.RUN_ID_number
- -r
- Pass the number of quartets to randomly sub-sample from the possible
number of quartets for the given taxon set. Only works in combination with
-f q !
- -s
- Specify the name of the BINARY alignment data file generated by the parser
component
- -S
- turn on memory saving option for gappy multi-gene alignments. For large
and gappy datasets specify -S to save memory This will produce
slightly different likelihood values, may be a bit slower but can reduce
memory consumption from 70GB to 19GB on very large and gappy datasets
- -t
- Specify a user starting tree file name in Newick format
- -v
- Display version information
- -w
- FULL (!) path to the directory into which ExaML shall write its output
files
- DEFAULT: current directory
- -Y
- Pass a quartet grouping file name defining four groups from which to draw
quartets The file input format must contain 4 groups in the following
form: (Chicken, Human, Loach), (Cow, Carp), (Mouse, Rat, Seal), (Whale,
Frog); Only works in combination with -f q !
--auto-prot=ml|bic|aic|aicc When using automatic
protein model selection you can chose the criterion for selecting these
models.
- RAxML will test all available prot subst. models except for LG4M, LG4X and
GTR-based models, with and without empirical base frequencies. You can
chose between ML score based selection and the BIC, AIC, and AICc
criteria.
- DEFAULT: ml
Alexandros Stamatakis, Andre J. Aberer, and Alexey Kozlov on
February 14 2017.
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.