NAME

       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

SYNOPSIS

       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]

OPTIONS

       -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

AUTHOR

       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.