FastML REST

FASTML REST interface: FASTML_XSEDE

This interface is used from the REST API to configure FASTML runs. .

The Tool ID for this interface is FASTML_XSEDE. It is selected with tool=FASTML_XSEDE

input.infile_ - Primary Input File
input.intree_ - Starting Tree in Newick Format (-intree)

vparam.runtime_ - Float - Maximum Hours to Run (up to 168 hours). default=0.5 h.
vparam.datatype_ - Excl - Specifyc the data type. Options: nuc (default); aa; codon
vparam.dna_matrix_ - Excl - Choose a DNA matrix (--SubMatrix); JC_Nuc (default); T92; HKY; GTR
vparam.protein_matrix_ - Excl - Choose a Protein matrix(--SubMatrix); JTT (default); LG; mtREV; cpREV; WAG; DAYHOFF;
vparam.codon_matrix_ - Excl - Choose a Codon matrix(--SubMatrix); yang (default); empiriCodon
vparam.optimize_branchlengths_ - Excl -  Optimize Branch Lengths (--OptimizeBL)
vparam.use_gamma_ -Switch - Use Gamma (--UseGamma), default = 1
vparam.opt_alpha_ - Switch - Optimize Alpha (-*OptAlpha), defaujlt = 1
vparam.specify_alpha_ - Float - Specify Alpha (--Alpha)
vparam.joint_reconstruction_ - Switch - Joint_reconstruction (--jointReconstruction)
vparam.indel_reconstruction_ - Excl - Method for Indel_reconstruction (--indelReconstruction); PARSIMONY; ML; BOTH
vparam.indel_cutoff_ - Float - Cutoff for Indel vs Char (--indelCutoff)

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