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RAxML Bootstrapping

Parameters for bootstrapping:

File Selection

Protein sequences		If not checked, DNA sequences will be assumed
Outgroup		The name of one or more (comma-separated) outgroup(s) can be specified
Substitution matrix	DAYHOFF DCMUT JTT MTREV WAG RTREV CPREV VT BLOSUM62 MTMAM
Use empirical base frequencies
Use a mixed/partioned model?		You may provide an alignment partition file
Per gene branch length optimization
Maximum likelihood search		Will search for best-scoring tree after the bootstraps
Estimate proportion of invariable sites
Random seed for bootstrapping
Random seed for parsimony inferences
Use a multifurcating constraint tree?		The name of a file that contains a multifurcating constraint tree. This tree does not have to be comprehensive
Automatically determine the number of bootstrapping runs		If checked, RAxML will automatically determine the point at which enough bootstrapping replicates have been produced
Number of bootstrapping runs

CIPRES is a Collaboration of the Following Institutions:
American Museum of Natural History, The University of Kansas, New Jersey Institute of Technology, North Carolina State University, Rice University, San Diego Supercomputer Center, Texas A&M, University of Arizona, University of British Columbia, University of California at Berkeley, University of California at San Diego, University of Connecticut, University of Pennsylvania, Univ. of South Carolina, University of Texas at Austin, and Yale University. xhtml | css