RAXML_LIGHT2
infile_ - Primary Input File
all_outputfiles_ - Results -
partition_ - InFile - Select a partition file that specifies mixed/partitioned model (-q. Optional)
estimate_branch_ - Switch - Estimate individual per-partition branch lengths (-M)
outgroup_ - String - Outgroup (one or more comma-separated outgroups, click link for syntax description)
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configure_model
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datatype_ - Excl - Sequence Type
dna_model_ - Excl - Model for Tree Inference with DNA data (-m)
prot_sub_model_ - Excl - Model for Tree Inference with Protein data (-m)
prot_matrix_spec_ - Excl - Protein Substitution Matrix
empirical_ - Excl - Use empirical base frequencies?
number_cats_ - Integer - Specify the number of distinct rate categories (-c, default = 25)
Section: ****************************************************************************
configure_search
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pars_hours_ - Integer - Maximum time in hours to generate a starting parsimony tree (default = 1 h; --parshours)
rsearch_seed_ - Integer - Set seed for generating first parsimony tree (-p, default = 12345)
num_rsearches_ - String - Number of regular searches to perform (-rsearches)
search_hours_ - Integer - Maximum time for a Search (default = 1 h)
use_mlsearchcc_ - Switch - Apply ML search convergence criterion to regular searches (-D)
num_bsearches_ - String - Number of bootstrap searches to perform (-bsearches)
bootstrap_seed_ - String - Provide a bootstrap seed (-b, default = 12345 )
aposterior_bootstopping_ - Excl - Select the criterion for a posteriori bootstopping analysis (-I)