raxmlHPC-PTHREADS-SSE3

USE(1)                           User Commands                          USE(1)



NAME
       Use - Randomized Axelerated Maximum Likelihood

DESCRIPTION
       Use raxml with AVX support (1 cpus)

       This is RAxML version 8.2.12 released by Alexandros Stamatakis on May
       2018.

       With greatly appreciated code contributions by: Andre Aberer
       (HITS) Simon Berger      (HITS) Alexey Kozlov     (HITS) Kassian Kobert
       (HITS) David Dao         (KIT and HITS) Sarah Lutteropp   (KIT and
       HITS) Nick Pattengale   (Sandia) Wayne Pfeiffer    (SDSC) Akifumi S.
       Tanabe (NRIFS) Charlie Taylor    (UF)

       Please also consult the RAxML-manual

       Please report bugs via the RAxML google group!  Please send us all
       input files, the exact invocation, details of the HW and operating
       system, as well as all error messages printed to screen.

       raxmlHPC[-SSE3|-AVX|-PTHREADS|-PTHREADS-SSE3|-PTHREADS-AVX|-HYBRID|-HYBRID-SSE3|HYBRID-AVX]

       -s sequenceFileName -n outputFileName -m substitutionModel

              [-a weightFileName] [-A secondaryStructureSubstModel] [-b
              bootstrapRandomNumberSeed] [-B wcCriterionThreshold] [-c
              numberOfCategories] [-C] [-d] [-D] [-e likelihoodEpsilon] [-E
              excludeFileName] [-f
              a|A|b|B|c|C|d|D|e|E|F|g|G|h|H|i|I|j|J|k|m|n|N|o|p|P|q|r|R|s|S|t|T|u|v|V|w|W|x|y]
              [-F] [-g groupingFileName] [-G placementThreshold] [-h] [-H] [-i
              initialRearrangementSetting] [-I
              autoFC|autoMR|autoMRE|autoMRE_IGN] [-j] [-J
              MR|MR_DROP|MRE|STRICT|STRICT_DROP|T_<PERCENT>] [-k] [-K] [-L
              MR|MRE|T_<PERCENT>] [-M] [-o
              outGroupName1[,outGroupName2[,...]]][-O] [-p
              parsimonyRandomSeed] [-P proteinModel] [-q
              multipleModelFileName] [-r binaryConstraintTree] [-R
              binaryModelParamFile] [-S secondaryStructureFile] [-t
              userStartingTree] [-T numberOfThreads] [-u] [-U] [-v] [-V] [-w
              outputDirectory] [-W slidingWindowSize] [-x
              rapidBootstrapRandomNumberSeed] [-X] [-y] [-Y
              quartetGroupingFileName|ancestralSequenceCandidatesFileName] [-z
              multipleTreesFile] [-#|-N
              numberOfRuns|autoFC|autoMR|autoMRE|autoMRE_IGN]
              [--mesquite][--silent][--no-seq-check][--no-bfgs]
              [--asc-corr=stamatakis|felsenstein|lewis]
              [--flag-check][--auto-prot=ml|bic|aic|aicc]
              [--epa-keep-placements=number][--epa-accumulated-threshold=threshold]
              [--epa-prob-threshold=threshold] [--JC69][--K80][--HKY85]
              [--bootstop-perms=number]

              [--quartets-without-replacement]

              [---without-replacement]

              [--print-identical-sequences]

       -a     Specify a column weight file name to assign individual weights
              to each column of the alignment. Those weights must be integers
              separated by any type and number of whitespaces whithin a
              separate file, see file "example_weights" for an example.

       -A     Specify one of the secondary structure substitution models
              implemented in RAxML.  The same nomenclature as in the PHASE
              manual is used, available models: S6A, S6B, S6C, S6D, S6E, S7A,
              S7B, S7C, S7D, S7E, S7F, S16, S16A, S16B

              DEFAULT: 16-state GTR model (S16)

       -b     Specify an integer number (random seed) and turn on
              bootstrapping

              DEFAULT: OFF

       -B     specify a floating point number between 0.0 and 1.0 that will be
              used as cutoff threshold for the MR-based bootstopping criteria.
              The recommended setting is 0.03.

              DEFAULT: 0.03 (recommended empirically determined setting)

       -c     Specify number of distinct rate catgories for RAxML when model
              of rate heterogeneity is set to CAT Individual per-site rates
              are categorized into numberOfCategories rate categories to
              accelerate computations.

              DEFAULT: 25

       -C     Enable verbose output for the "-L" and "-f i" options. This will
              produce more, as well as more verbose output files

              DEFAULT: OFF

       -d     start ML optimization from random starting tree

              DEFAULT: OFF

       -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 tree topology

       DEFAULT: 0.1
              for models not using proportion of invariant sites estimate

              0.001 for models using proportion of invariant sites estimate

       -E     specify an exclude file name, that contains a specification of
              alignment positions you wish to exclude.  Format is similar to
              Nexus, the file shall contain entries like "100-200 300-400", to
              exclude a single column write, e.g., "100-100", if you use a
              mixed model, an appropriately adapted model file will be
              written.

       -f     select algorithm:

              "-f a": rapid Bootstrap analysis and search for best-scoring ML
              tree in one program run "-f A": compute marginal ancestral
              states on a ROOTED reference tree provided with "-t" "-f b":
              draw bipartition information on a tree provided with "-t" based
              on multiple trees

              (e.g., from a bootstrap) in a file specified by "-z"

       "-f B": optimize br-len scaler and other model parameters (GTR, alpha,
       etc.) on a tree provided with "-t".
              The tree needs to contain branch lengths. The branch lengths
              will not be optimized, just scaled by a single common value.

              "-f c": check if the alignment can be properly read by RAxML "-f
              C": ancestral sequence test for Jiajie, users will also need to
              provide a list of taxon names via -Y separated by whitespaces
              "-f d": new rapid hill-climbing

              DEFAULT: ON

              "-f D": rapid hill-climbing with RELL bootstraps "-f e":
              optimize model+branch lengths for given input tree under
              GAMMA/GAMMAI only "-f E": execute very fast experimental tree
              search, at present only for testing "-f F": execute fast
              experimental tree search, at present only for testing "-f g":
              compute per site log Likelihoods for one or more trees passed
              via

       "-z" and write them to a file that can be read by CONSEL
              The model parameters will be estimated on the first tree only!

       "-f G": compute per site log Likelihoods for one or more trees passed
       via
              "-z" and write them to a file that can be read by CONSEL.  The
              model parameters will be re-estimated for each tree

       "-f h": compute log likelihood test (SH-test) between best tree passed
       via "-t"
              and a bunch of other trees passed via "-z" The model parameters
              will be estimated on the first tree only!

       "-f H": compute log likelihood test (SH-test) between best tree passed
       via "-t"
              and a bunch of other trees passed via "-z" The model parameters
              will be re-estimated for each tree

       "-f i": calculate IC and TC scores (Salichos and Rokas 2013) on a tree
       provided with "-t" based on multiple trees
              (e.g., from a bootstrap) in a file specified by "-z"

       "-f I": a simple tree rooting algorithm for unrooted trees.
              It roots the tree by rooting it at the branch that best balances
              the subtree lengths (sum over branches in the subtrees) of the
              left and right subtree.  A branch with an optimal balance does
              not always exist!  You need to specify the tree you want to root
              via "-t".

       "-f j": generate a bunch of bootstrapped alignment files from an
       original alignemnt file.
              You need to specify a seed with "-b" and the number of
              replicates with "-#"

              "-f J": Compute SH-like support values on a given tree passed
              via "-t".  "-f k": Fix long branch lengths in partitioned data
              sets with missing data using the

       branch length stealing algorithm.
              This option only works in conjunction with "-t", "-M", and "-q".
              It will print out a tree with shorter branch lengths, but having
              the same likelihood score.

       "-f m": compare bipartitions between two bunches of trees passed via
       "-t" and "-z"
              respectively. This will return the Pearson correlation between
              all bipartitions found in the two tree files. A file called
              RAxML_bipartitionFrequencies.outpuFileName will be printed that
              contains the pair-wise bipartition frequencies of the two sets

       "-f n": compute the log likelihood score of all trees contained in a
       tree file provided by
              "-z" under GAMMA or GAMMA+P-Invar The model parameters will be
              estimated on the first tree only!

       "-f N": compute the log likelihood score of all trees contained in a
       tree file provided by
              "-z" under GAMMA or GAMMA+P-Invar The model parameters will be
              re-estimated for each tree

              "-f o": old and slower rapid hill-climbing without heuristic
              cutoff "-f p": perform pure stepwise MP addition of new
              sequences to an incomplete starting tree and exit "-f P":
              perform a phylogenetic placement of sub trees specified in a
              file passed via "-z" into a given reference tree

              in which these subtrees are contained that is passed via "-t"
              using the evolutionary placement algorithm.

              "-f q": fast quartet calculator "-f r": compute pairwise
              Robinson-Foulds (RF) distances between all pairs of trees in a
              tree file passed via "-z"

       if the trees have node labales represented as integer support values
       the program will also compute two flavors of
              the weighted Robinson-Foulds (WRF) distance

       "-f R": compute all pairwise Robinson-Foulds (RF) distances between a
       large reference tree
              passed via "-t"

       and many smaller trees (that must have a subset of the taxa of the
       large tree) passed via "-z".
              This option is intended for checking the plausibility of very
              large phylogenies that can not be inspected visually any more.

              "-f s": split up a multi-gene partitioned alignment into the
              respective subalignments "-f S": compute site-specific placement
              bias using a leave one out test inspired by the evolutionary
              placement algorithm "-f t": do randomized tree searches on one
              fixed starting tree "-f T": do final thorough optimization of ML
              tree from rapid bootstrap search in stand-alone mode "-f u":
              execute morphological weight calibration using maximum
              likelihood, this will return a weight vector.

              you need to provide a morphological alignment and a reference
              tree via "-t"

       "-f v": classify a bunch of environmental sequences into a reference
       tree using thorough read insertions
              you will need to start RAxML with a non-comprehensive reference
              tree and an alignment containing all sequences (reference +
              query)

       "-f V": classify a bunch of environmental sequences into a reference
       tree using thorough read insertions
              you will need to start RAxML with a non-comprehensive reference
              tree and an alignment containing all sequences (reference +
              query) WARNING: this is a test implementation for more efficient
              handling of multi-gene/whole-genome datasets!

       "-f w": compute ELW test on a bunch of trees passed via "-z"
              The model parameters will be estimated on the first tree only!

       "-f W": compute ELW test on a bunch of trees passed via "-z"
              The model parameters will be re-estimated for each tree

       "-f x": compute pair-wise ML distances, ML model parameters will be
       estimated on an MP
              starting tree or a user-defined tree passed via "-t", only
              allowed for GAMMA-based models of rate heterogeneity

       "-f y": classify a bunch of environmental sequences into a reference
       tree using parsimony
              you will need to start RAxML with a non-comprehensive reference
              tree and an alignment containing all sequences (reference +
              query)

              DEFAULT for "-f": new rapid hill climbing

       -F     enable ML tree searches under CAT model for very large trees
              without switching to GAMMA in the end (saves memory).  This
              option can also be used with the GAMMA models in order to avoid
              the thorough optimization of the best-scoring ML tree in the
              end.

              DEFAULT: OFF

       -g     specify the file name of a multifurcating constraint tree this
              tree does not need to be comprehensive, i.e. must not contain
              all taxa

       -G     enable the ML-based evolutionary placement algorithm heuristics
              by specifiyng a threshold value (fraction of insertion branches
              to be evaluated using slow insertions under ML).

       -h     Display this help message.

       -H     Disable pattern compression.

              DEFAULT: ON

       -i     Initial rearrangement setting for the subsequent application of
              topological changes phase

       -I     a posteriori bootstopping analysis. Use:

              "-I autoFC" for the frequency-based criterion "-I autoMR" for
              the majority-rule consensus tree criterion "-I autoMRE" for the
              extended majority-rule consensus tree criterion "-I autoMRE_IGN"
              for metrics similar to MRE, but include bipartitions under the
              threshold whether they are compatible

              or not. This emulates MRE but is faster to compute.

              You also need to pass a tree file containg several bootstrap
              replicates via "-z"

       -j     Specifies that intermediate tree files shall be written to file
              during the standard ML and BS tree searches.

              DEFAULT: OFF

       -J     Compute majority rule consensus tree with "-J MR" or extended
              majority rule consensus tree with "-J MRE" or strict consensus
              tree with "-J STRICT". For a custom consensus threshold >= 50%,
              specify T_<NUM>, where 100 >= NUM >= 50.  Options "-J
              STRICT_DROP" and "-J MR_DROP" will execute an algorithm that
              identifies dropsets which contain rogue taxa as proposed by
              Pattengale et al. in the paper "Uncovering hidden phylogenetic
              consensus".  You will also need to provide a tree file
              containing several UNROOTED trees via "-z"

       -k     Specifies that bootstrapped trees should be printed with branch
              lengths.  The bootstraps will run a bit longer, because model
              parameters will be optimized at the end of each run under GAMMA
              or GAMMA+P-Invar respectively.

              DEFAULT: OFF

       -K     Specify one of the multi-state substitution models (max 32
              states) implemented in RAxML.  Available models are: ORDERED,
              MK, GTR

              DEFAULT: GTR model

       -L     Compute consensus trees labelled by IC supports and the overall
              TC value as proposed in Salichos and Rokas 2013.  Compute a
              majority rule consensus tree with "-L MR" or an extended
              majority rule consensus tree with "-L MRE".  For a custom
              consensus threshold >= 50%, specify "-L T_<NUM>", where 100 >=
              NUM >= 50.  You will of course also need to provide a tree file
              containing several UNROOTED trees via "-z"!

       -m     Model of Binary (Morphological), Nucleotide, Multi-State, or
              Amino Acid Substitution:

              BINARY:

       "-m BINCAT[X]"
              : Optimization of site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency. Final tree
              might be evaluated automatically under BINGAMMA, depending on
              the tree search option.  With the optional "X" appendix you can
              specify a ML estimate of base frequencies.

       "-m BINCATI[X]"
              : Optimization of site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency. Final tree
              might be evaluated automatically under BINGAMMAI, depending on
              the tree search option.  With the optional "X" appendix you can
              specify a ML estimate of base frequencies.

       "-m ASC_BINCAT[X]"
              : Optimization of site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency. Final tree
              might be evaluated automatically under BINGAMMA, depending on
              the tree search option.  With the optional "X" appendix you can
              specify a ML estimate of base frequencies.  The ASC prefix willl
              correct the likelihood for ascertainment bias.

       "-m BINGAMMA[X]"
              : GAMMA model of rate heterogeneity (alpha parameter will be
              estimated).

              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

       "-m ASC_BINGAMMA[X]" : GAMMA model of rate heterogeneity (alpha
       parameter will be estimated).
              The ASC prefix willl correct the likelihood for ascertainment
              bias.  With the optional "X" appendix you can specify a ML
              estimate of base frequencies.

       "-m BINGAMMAI[X]"
              : Same as BINGAMMA, but with estimate of proportion of
              invariable sites.

              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

              NUCLEOTIDES:

       "-m GTRCAT[X]"
              : GTR + Optimization of substitution rates + Optimization of
              site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency.  Final
              tree might be evaluated under GTRGAMMA, depending on the tree
              search option.  With the optional "X" appendix you can specify a
              ML estimate of base frequencies.

       "-m GTRCATI[X]"
              : GTR + Optimization of substitution rates + Optimization of
              site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency.  Final
              tree might be evaluated under GTRGAMMAI, depending on the tree
              search option.  With the optional "X" appendix you can specify a
              ML estimate of base frequencies.

       "-m ASC_GTRCAT[X]"
              : GTR + Optimization of substitution rates + Optimization of
              site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency.  Final
              tree might be evaluated under GTRGAMMA, depending on the tree
              search option.  With the optional "X" appendix you can specify a
              ML estimate of base frequencies.  The ASC prefix willl correct
              the likelihood for ascertainment bias.

       "-m GTRGAMMA[X]"
              : GTR + Optimization of substitution rates + GAMMA model of rate

       heterogeneity (alpha parameter will be estimated).
              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

       "-m ASC_GTRGAMMA[X]" : GTR + Optimization of substitution rates + GAMMA
       model of rate
              heterogeneity (alpha parameter will be estimated).  The ASC
              prefix willl correct the likelihood for ascertainment bias.
              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

       "-m GTRGAMMAI[X]"
              : Same as GTRGAMMA, but with estimate of proportion of
              invariable sites.

              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

              MULTI-STATE:

       "-m MULTICAT[X]"
              : Optimization of site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency. Final tree
              might be evaluated automatically under MULTIGAMMA, depending on
              the tree search option.  With the optional "X" appendix you can
              specify a ML estimate of base frequencies.

       "-m MULTICATI[X]"
              : Optimization of site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency. Final tree
              might be evaluated automatically under MULTIGAMMAI, depending on
              the tree search option.  With the optional "X" appendix you can
              specify a ML estimate of base frequencies.

       "-m ASC_MULTICAT[X]"
              : Optimization of site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency. Final tree
              might be evaluated automatically under MULTIGAMMA, depending on
              the tree search option.  With the optional "X" appendix you can
              specify a ML estimate of base frequencies.  The ASC prefix willl
              correct the likelihood for ascertainment bias.

       "-m MULTIGAMMA[X]"
              : GAMMA model of rate heterogeneity (alpha parameter will be
              estimated).

              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

       "-m ASC_MULTIGAMMA[X]" : GAMMA model of rate heterogeneity (alpha
       parameter will be estimated).
              The ASC prefix willl correct the likelihood for ascertainment
              bias.  With the optional "X" appendix you can specify a ML
              estimate of base frequencies.

       "-m MULTIGAMMAI[X]"
              : Same as MULTIGAMMA, but with estimate of proportion of
              invariable sites.

              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

              You can use up to 32 distinct character states to encode
              multi-state regions, they must be used in the following order:
              0, 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K,
              L, M, N, O, P, Q, R, S, T, U, V i.e., if you have 6 distinct
              character states you would use 0, 1, 2, 3, 4, 5 to encode these.
              The substitution model for the multi-state regions can be
              selected via the "-K" option

              AMINO ACIDS:

       "-m PROTCATmatrixName[F|X]"
              : specified AA matrix + Optimization of substitution rates +
              Optimization of site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency.   Final
              tree might be evaluated automatically under
              PROTGAMMAmatrixName[F|X], depending on the tree search option.
              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

       "-m PROTCATImatrixName[F|X]"
              : specified AA matrix + Optimization of substitution rates +
              Optimization of site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency.   Final
              tree might be evaluated automatically under
              PROTGAMMAImatrixName[F|X], depending on the tree search option.
              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

       "-m ASC_PROTCATmatrixName[F|X]"
              : specified AA matrix + Optimization of substitution rates +
              Optimization of site-specific

       evolutionary rates which are categorized into numberOfCategories
       distinct
              rate categories for greater computational efficiency.   Final
              tree might be evaluated automatically under
              PROTGAMMAmatrixName[F|X], depending on the tree search option.
              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.  The ASC prefix willl correct the likelihood
              for ascertainment bias.

       "-m PROTGAMMAmatrixName[F|X]"
              : specified AA matrix + Optimization of substitution rates +
              GAMMA model of rate

       heterogeneity (alpha parameter will be estimated).
              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

       "-m ASC_PROTGAMMAmatrixName[F|X]" : specified AA matrix + Optimization
       of substitution rates + GAMMA model of rate
              heterogeneity (alpha parameter will be estimated).  The ASC
              prefix willl correct the likelihood for ascertainment bias.
              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

       "-m PROTGAMMAImatrixName[F|X]"
              : Same as PROTGAMMAmatrixName[F|X], but with estimate of
              proportion of invariable sites.

              With the optional "X" appendix you can specify a ML estimate of
              base frequencies.

              Available AA substitution models: DAYHOFF, DCMUT, JTT, MTREV,
              WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, LG, MTART, MTZOA, PMB,
              HIVB, HIVW, JTTDCMUT, FLU, STMTREV, DUMMY, DUMMY2, AUTO, LG4M,
              LG4X, PROT_FILE, GTR_UNLINKED, GTR With the optional "F"
              appendix you can specify if you want to use empirical base
              frequencies.  AUTOF and AUTOX are not supported any more, if you
              specify AUTO it will test prot subst. models with and without
              empirical base frequencies now!  Please note that for
              partitioned models you can in addition specify the per-gene AA
              model in the partition file (see manual for details). Also note
              that if you estimate AA GTR parameters on a partitioned dataset,
              they will be linked (estimated jointly) across all partitions to
              avoid over-parametrization

       -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.

       -o     Specify the name of a single outgroup or a comma-separated list
              of outgroups, eg "-o Rat" or "-o Rat,Mouse", in case that
              multiple outgroups are not monophyletic the first name in the
              list will be selected as outgroup, don't leave spaces between
              taxon names!

       -O     Disable check for completely undetermined sequence in alignment.
              The program will not exit with an error message when "-O" is
              specified.

              DEFAULT: check enabled

       -p     Specify a random number seed for the parsimony inferences. This
              allows you to reproduce your results and will help me debug the
              program.

       -P     Specify the file name of a user-defined AA (Protein)
              substitution model. This file must contain 420 entries, the
              first 400 being the AA substitution rates (this must be a
              symmetric matrix) and the last 20 are the empirical base
              frequencies

       -q     Specify the file name which contains the assignment of models to
              alignment partitions for multiple models of substitution. For
              the syntax of this file please consult the manual.

       -r     Specify the file name of a binary constraint tree.  this tree
              does not need to be comprehensive, i.e. must not contain all
              taxa

       -R     Specify the file name of a binary model parameter file that has
              previously been generated with RAxML using the -f e tree
              evaluation option. The file name should be:
              RAxML_binaryModelParameters.runID

       -s     Specify the name of the alignment data file in PHYLIP format

       -S     Specify the name of a secondary structure file. The file can
              contain "." for alignment columns that do not form part of a
              stem and characters "()<>[]{}" to define stem regions and
              pseudoknots

       -t     Specify a user starting tree file name in Newick format

       -T     PTHREADS VERSION ONLY! Specify the number of threads you want to
              run.  Make sure to set "-T" to at most the number of CPUs you
              have on your machine, otherwise, there will be a huge
              performance decrease!

       -u     use the median for the discrete approximation of the GAMMA model
              of rate heterogeneity

              DEFAULT: OFF

       -U     Try to save memory by using SEV-based implementation for gap
              columns on large gappy alignments The technique is described
              here: http://www.biomedcentral.com/1471-2105/12/470 This will
              only work for DNA and/or PROTEIN data and only with the SSE3 or
              AVX-vextorized version of the code.

       -v     Display version information

       -V     Disable rate heterogeneity among sites model and use one without
              rate heterogeneity instead.  Only works if you specify the CAT
              model of rate heterogeneity.

              DEFAULT: use rate heterogeneity

       -w     FULL (!) path to the directory into which RAxML shall write its
              output files

              DEFAULT: current directory

       -W     Sliding window size for leave-one-out site-specific placement
              bias algorithm only effective when used in combination with "-f
              S"

              DEFAULT: 100 sites

       -x     Specify an integer number (random seed) and turn on rapid
              bootstrapping CAUTION: unlike in version 7.0.4 RAxML will
              conduct rapid BS replicates under the model of rate
              heterogeneity you specified via "-m" and not by default under
              CAT

       -X     Same as the "-y" option below, however the parsimony search is
              more superficial.  RAxML will only do a randomized stepwise
              addition order parsimony tree reconstruction without performing
              any additional SPRs.  This may be helpful for very broad
              whole-genome datasets, since this can generate topologically
              more different starting trees.

              DEFAULT: OFF

       -y     If you want to only compute a parsimony starting tree with RAxML
              specify "-y", the program will exit after computation of the
              starting tree

              DEFAULT: OFF

       -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 !

       -z     Specify the file name of a file containing multiple trees e.g.
              from a bootstrap that shall be used to draw bipartition values
              onto a tree provided with "-t", It can also be used to compute
              per site log likelihoods in combination with "-f g" and to read
              a bunch of trees for a couple of other options ("-f h", "-f m",
              "-f n").

       -#|-N  Specify the number of alternative runs on distinct starting
              trees In combination with the "-b" option, this will invoke a
              multiple boostrap analysis Note that "-N" has been added as an
              alternative since "-#" sometimes caused problems with certain
              MPI job submission systems, since "-#" is often used to start
              comments.  If you want to use the bootstopping criteria specify
              "-# autoMR" or "-# autoMRE" or "-# autoMRE_IGN" for the
              majority-rule tree based criteria (see -I option) or "-# autoFC"
              for the frequency-based criterion.  Bootstopping will only work
              in combination with "-x" or "-b"

              DEFAULT: 1 single analysis

       --mesquite Print output files that can be parsed by Mesquite.

              DEFAULT: Off

       --silent Disables printout of warnings related to identical sequences
              and entirely undetermined sites in the alignment

              DEFAULT: Off

       --no-seq-check Disables checking the input MSA for identical sequences
       and entirely undetermined sites.
              Enabling this option may save time, in particular for large
              phylogenomic alignments.  Before using this, make sure to check
              the alignment using the "-f c" option!

              DEFAULT: Off

       --no-bfgs Disables automatic usage of BFGS method to optimize GTR rates
              on unpartitioned DNA datasets

              DEFAULT: BFGS on

       --asc-corr Allows to specify the type of ascertainment bias correction
              you wish to use. There are 3

              types available: --asc-corr=lewis: the standard correction by
              Paul Lewis --asc-corr=felsenstein: a correction introduced by
              Joe Felsenstein that allows to explicitely specify

              the number of invariable sites (if known) one wants to correct
              for.

       --asc-corr=stamatakis: a correction introduced by myself that allows to
       explicitely specify
              the number of invariable sites for each character (if known) one
              wants to correct for.

       --flag-check When using this option, RAxML will only check if all
              command line flags specifed are available and then exit

              with a message listing all invalid command line flags or with a
              message stating that all flags are valid.

       --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

       --epa-keep-placements=number specify the number of potential placements
              you want to keep for each read in the EPA algorithm.

              Note that, the actual values printed will also depend on the
              settings for --epa-prob-threshold=threshold !

              DEFAULT: 7

       --epa-prob-threshold=threshold specify a percent threshold for
              including potential placements of a read depending on the

              maximum placement weight for this read. If you set this value to
              0.01 placements that have a placement weight of 1 per cent of
              the maximum placement will still be printed to file if the
              setting of --epa-keep-placements allows for it

              DEFAULT: 0.01

       --epa-accumulated-threshold=threshold specify an accumulated likelihood
              weight threshold for which different placements of read are
              printed

              to file. Placements for a read will be printed until the sum of
              their placement weights has reached the threshold value.  Note
              that, this option can neither be used in combination with
              --epa-prob-threshold nor with --epa-keep-placements!

       --JC69 specify that all DNA partitions will evolve under the
              Jukes-Cantor model, this overrides all other model
              specifications for DNA partitions.

              DEFAULT: Off

       --K80 specify that all DNA partitions will evolve under the K80 model,
              this overrides all other model specifications for DNA
              partitions.

              DEFAULT: Off

       --HKY85 specify that all DNA partitions will evolve under the HKY85
              model, this overrides all other model specifications for DNA
              partitions.

              DEFAULT: Off

       --bootstop-perms=number specify the number of permutations to be
              conducted for the bootstopping/bootstrap convergence test.

              The allowed minimum number is 100!

              DEFAULT: 100

       --quartets-without-replacement specify that quartets are randomly
              subsampled, but without replacement.

              DEFAULT: random sampling with replacements

       --print-identical-sequences specify that RAxML shall automatically
              generate a .reduced alignment with all

              undetermined columns removed, but without removing exactly
              identical sequences

              DEFAULT: identical sequences will also be removed in the
              .reduced file

       This is RAxML version 8.2.12 released by Alexandros Stamatakis on May
       2018.

       With greatly appreciated code contributions by: Andre Aberer
       (HITS) Simon Berger      (HITS) Alexey Kozlov     (HITS) Kassian Kobert
       (HITS) David Dao         (KIT and HITS) Sarah Lutteropp   (KIT and
       HITS) Nick Pattengale   (Sandia) Wayne Pfeiffer    (SDSC) Akifumi S.
       Tanabe (NRIFS) Charlie Taylor    (UF)



Use raxml with AVX support (1 cpus)June 2018                            USE(1)