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Start Your TrialRAxML-NG is a successor of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood computation implemented in libpll (Flouri et al. 2014).
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.
RAxML-NG offers improvements in speed, flexibility and user-friendliness over the previous RAxML versions. It also implements some of the features previously available in ExaML (Kozlov et al. 2015), including checkpointing and efficient load balancing for partitioned alignments (Kobert et al. 2014). We note that most of the options available through RAxML NG have direct counterparts in the original RAxML. We also note that the --all option in RAxML NG can be much slower than the -f A option in RAxML.
Configuring the analysis
RAXMLNG_XSEDE Parameter Summary:
Note that when the term “Excl” follows a parameter name, it means that only one of several possible values are accepted. The accepted values are listed with the parameter. The term “Switch” means that only 0 or 1 are accepted, and the expression either evaluates to true or false. Other parameter type terms, such as Integer, String, Float, etc are self-explanatory.
Input File Parameters:
Input File Parameters must be accompanied by an upload file (see RAxML-NG manual for format):
input.infile_ - InFile - Supply a matrix
input.constraint_ - InFile - Constraint tree (--tree-constraint)
input.partition_file_ - InFile - Use a mixed/partitioned model? (-q)
input.rates_file_ - InFile - Select a custom rates file; If you upload a file here, use the free text box to specify your model, and use the format: model{rates.txt}, for example PROTGTR{rates.txt}
input.paml_file_ - InFile - Select a paml file. If you upload a file here, use the free text box to specify your paml file, and use the format: model{paml.txt}, for example PROTGTR{paml.txt}
input.character_file_ - InFile - Select a custom character map file; If you upload a file here, use the free text box to specify +M{charmap.txt}
input.empirical_file_ - InFile - Select empirical base frequencies file when empirical eq_ +FU{freqs.txt}
input.besttree_upload_ - InFile - Upload tree for terrace or ancestral analysis; for fa or terrace analysis.
input.alltrees_upload_ - InFile - Upload set of trees for RF or a consense analysis; when select_analysis_= J or | rfdist
input.referencetree_upload_ - Provide a tree to evaluate, or for calculating support (--tree); when select_analysis_ = evaluate or fb
input.bootstrapstree_upload_ - Upload a set of bootstrap trees for support option or a posteriori analysis; when select_analysis_ = I or fb
input.startingtree_upload_ - Upload a custom starting tree
Visible Parameters:
General run characteristics:
vparam.runtime_ - Float - less than 168, default = 0.25
vparam.datatype_ - Excl - Sequence Type; protein, dna, bin, multi, unphased; default = dna
vparam.num_patterns_ Integer - Number of patterns in your data set!defined $num_patterns
vparam.select_analysis_ - Excl - Select the Analysis Type: all, bootstrap, fc, search, search1, fb, fA, evaluate, fJ, loglh, parse, rfdist, I, J , y, terrace
vparam.specify_bootstraps_ - Integer - Specify the number of bootstraps (only wehn select_analysis_ = all, bootstrap, and fJ; default = 100
vparam.specify_bscutoff_ - Float - Specify the bootstrap cutoff value No default.
vparam.specify_bsmetric_ - Excl - Specify the branch support metric (bs-metric); only when select_analysis_ = fJ, all, or bootstrap. fpd,tbe, or both; default = fbp
vparam.enable_modelparamopt_ - Switch - Enable model parameter optimization; only when select_analysis = evaluate; default = 0
vparam.enable_brlopt_ - Switch - Enable branch length optimization only when select_analysis = evaluate; default = 0
vparam.outgroup_ - String - Specify an outproup (one or more comma-separated outgroups) No white space is allowed.
vparam.outprefix_ String - Prefix for Output
vparam.specify_seed_ - Integer - Specify a value for the seed (--seed)
vparam.more_memory_ - Switch - More memory. Runs on a high memory node 1080G
Substitution Matrix Options
Matrix model specification for a whole data set can be acocmplished in two ways: you can select a model from the options here; or you can enter it via free text using the any_matrix_spec_ option. If there is more than one model, you specify that using a partition file. An uploaded partition file turns off all options. To use these options you must have selected the correct datatype.
vparam.dna_gtrcat_ - String - Choose a nucleotide model; JC, K80, F81, HKY, TN93ef, TN93, K81, K81uf, TPM2, TPM2uf, TPM3, TPM3uf, TIM1, TIM1uf, TIM2, TIM2uf, TIM3, TIM3uf, TVMef, TVM, SYM, GTR, default=GTR
vparam.prot_matrix_spec_ - String - Protein Substitution Matrix; Blosum62, cpREV, Dayhoff, DCMut, DEN, FLU, HIVb,HIVw, JTT, JTT-DCMut, LG, mtART,mtMAM, mtREV, mtZOA, PMB, rtREV,stmtREV, VT, WAG, LG4M (implies +G4), LG4X (implies +R4), PROTGTR; default = JTT. when datatype_=protein
vparam.bin_matrix_spec_ - String - Binary Substitution Matrix (automatic, there is only one option) used when datatype=bin.
vparam.state_value_ - Integer - Number of states for Morphological/Multistate Model; when datatype_ is multi;
vparam.multimodel_value_ - Excl - Model for Morphological/Multistate; when datatype_ is multi; MK or GTR.
vparam.unphased_value_ - Excl - Model for Unphased diploid genotypes; when datatype=unphased_ ; GTJC; GTHKY4; GTGTR4; GTGTR
vparam.any_matrix_spec_ - String - Specify your model in free text. YOu can specify any valid model here.
vparam.select_brlength_ - Excl - Select branch length estimation method (--brlen) when a partiton file is specified. linked; scaled; unlinked; default = scaled
Among Site Rate Heterogeneity Options
vparam.ratehet_model_ - Excl - Among-site rate heterogeneity model; when mlsearch_ = 1; +G; +GA; +Gn; Gna; +Rn; Rnr
vparam.num_categories_ - Integer - Specify the number of categories
vparam.specify_alpha_ - Float - Specify alpha; required when ratehet_model_ = Gna
vparam.specify_rates_ - Float - Specify the rates; required when ratehet_model_ = Rnr
vparam.specify_weights_ - Float - Specify the weights; required when ratehet_model_ = Rnr
Model Options
vparam.invariable_ - Excl - Estimate proportion of invariable sites ( + I); when mlsearch_ = 1; +IO; +IC
vparam.userdefined_invariable_ - String - Enter the user-defined invariable data: enter {p}; invariable_ cannot be defined for this.
This parameter adds the string +IU{p} to the command line, where p is the user defined invariable parameter. Enter the just the value of p here, and the application will place it inside the curly braces for you, eg, if you enter x the command line will print as +IU{x}.
vparam.empirical_ - Excl - Specify empirical base frequencies; +FC; +FO; +FE; +FU{freqs.txt}
Ascertainment Bias Confguration; only when invariable = 0; only one tpye of correction per run
vparam.ascl_ - Excl - Lewis Correction for Ascertainment bias (ASC_); +ASC_LEWIS or no entry;
vparam.ascf_ -String - Enter Felsenstein Correction for Ascertainment bias (ASC_)
vparam.ascs_ - String - Enter Stamatakis Correction for Ascertainment bias (ASC_)
Starting Tree Options
vparam.starting_parstree_ - Integer - Number of parsimony starting trees (constraint_ not allowed)
vparam.starting_randtree_ - Integer - Number of random starting trees
Log Verbosity
vparam.setlogVerbosity_ - Excl - Set the log verbosity (--log xxx); ERROR; WARNING; RESULT; INFO; PROGRESS; VERBOSE; DEBUG
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