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Start Your TrialThis is one of several RAxML interfaces that can be used from the REST API. Others include raxmlhpc2_tgb.xml, raxmlhpc8_rest_xsede.xml, and raxmlhpc2_workflow.xml. This interface is a supported legacy interface. If you are starting a new client or service, please use raxmlhpc8_rest_xsede.xml. It will be much easier to use.
The tool id for this interface is RAXMLHPC2_BB. It is selected with toolId=RAXMHPC2__BB
Supported parameters for tool=RAXMLHPC2_BB that require input files are:
input.infile_ - InFile - Primary Input File
input.binary_backbone_ - InFile - Binary Backbone (-r)
input.partition_ - InFile - Use a mixed/partitioned model? (-q)
input.exclude_file_ - InFile - Choose an input file that excludes the range of positions specifed in this file (-E)
input.constraint_ - InFile - Constraint (-g).
Other supported parameters for tool=RAXMLHPC2_BB are:
vparam.runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly) default=0.25, max = 168
vparam.datatype_ - Excl - Sequence Type default=dna, allowed dna, protein
vparam.outgroup_ - String - Outgroup (one or more comma-separated outgroups, no blank spaces)
vparam.invariable_ - Excl - Estimate proportion of invariable sites (GTRGAMMA + I) defult=null; I or null.
vparam.prot_matrix_spec_ - Excl - Protein Substitution Matrix default=JTT, allowed=DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62., MTMAM, LG, GTR
vparam.empirical_ - Excl - Use empirical base frequencies? (default=null, allowed: F or null)
vparam.mlsearch_ - Switch - Find best tree using maximum likelihood search (default=1)
vparam.use_bootstopping_ - Switch - Let RAxML halt bootstrapping automatically (HIGHLY recommended) default=1
vparam.no_bfgs_ - Switch - Don't use BFGS searching algorithm (--no-bfgs) default=0
vparam.printbrlength_ - Switch - Print branch lengths (-k) default=0
If there is a tool or a feature you need, please let us know