PHYLOBAYES_XSEDE
infile_ - Primary Input File
ALL_FILES_ - Results -
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
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bryan_script
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set_seed_ - Integer - Enter seed value
checkinterval_ - Integer - Number of seconds to wait between checks for convergence.
burninval_ - Integer - Number of cycles to exclude from convergence checks.
acceptdiffval_ - Float - Maximum \maxdiff" value to accept.
acceptsizeval_ - Integer - Minimum Effective Size
giveupval_ - Integer - Minimum number of cycles before giving up if "maxdiff" is still 1 (Analysis is stuck)
Section: ****************************************************************************
bryan_script
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constant_sitesr_ - Switch - Remove Constant Sites (-dc)
starting_tree_ - InFile - Specify a Newick Starting Tree (-tree)
constraint_tree_ - InFile - Specify a fixed topology (in the selected file)(-T)
saving_freq_ - Integer - Save every (-x)
stop_at_ - Integer - Number of points after which the chain should stop (-1 = forever)
save_detmodelconf_ - Switch - Save detailed model configuration for each point(-s)
Section: ****************************************************************************
evolutionary_models
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num_gammacats_ - Integer - Number of Categories for the discrete gamma distribution (-dgam)
exchange_rates_ - Excl - Exchange Rates
custom_exch_ - Switch - Provide a custom exchange rate file
custom_exch_file_ - InFile - Select the Custom Exchangabilities File
profile_mixture_ - Excl - Profile Mixture
predefined_profiles_ - Excl - Choose a Predefined Profile
custom_profile_ - InFile - Select the Custom Exchangabilities File
mutsel_model_ - Switch - Use Codon Alignments Only
mtvert_codons_ - Switch - Use Vertebrate Mitochondrial Genetic Code