## DormanResearch : CBrotherManualReferers: cBrother :: (Remote :: Orphans :: Tree ) |
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Dorman Lab Wiki |

- Preliminaries
- Tutorial or Worked Examples
- Data
- Priors
- Processing cBrother Output
- Command File Options: The command file options are listed more-or-less in the order of greatest utility. If links are not included, the description here should suffice
- Controlling how cBrother runs: Use these commands to set the properties of the MCMC run.
- length: set the length of the MCMC run
- burnin: set the length of the MCMC burnin
- subsample: set the subsample rate for the MCMC run
- continue: set to continue a previous MCMC run (part of checkpointing)
- cmdfile_errors: determine how errors in the command file format will be reported

- Controlling the model and topology space cBrother uses
- model: select the type of model/analysis
- change_points: set the types of allowable change points
- allow_split_ancestry: allow or exclude certain types of topologies from the list of possibilities
- allow_ancient_ancestry: allow or exclude certain types of topologies from the list of possibilities
- parent_tree: fixed genotype tree
- number_of_clades: specify the number of genotypes in the data
- clade: define the sequences belonging to a genotype

- Controlling what cBrother outputs
- output_style: set the output style
- stdout_style: set the style for the screen output
- decorate_output: add slightly more human-friendly information to output file
- stdout_during_burnin: output progress to the screen during the burnin
- debug: set the level of debugging output
- output_topology_list: specify where the topology list is to be output, if anywhere

- Controlling cBrother Priors
- hky_kappa_prior: set the prior distribution on the HKY transition/transversion ratio.
- hky_kappa_prior_max?: when the HKY transition/transversion ratio prior is uniform, this is the prior maximum.
- hky_kappa_prior_mean?: when the HKY transition/transversion ratio prior is exponential, this is the prior mean.
- hky_kappa_prior_log_mean?: when the HKY transition/transversion ratio prior is lognormal, this is the prior log mean.
- hky_kappa_prior_variance?: when the HKY transition/transversion ratio prior is lognormal, this is the prior log variance.
- hky_kappa_hyper_prior?: specify whether the HKY transition/transversion hyperprior parameters are estimated or fixed.
- integrated_branch_prior: set the prior distribution on the HKY transition/transversion ratio.
- integrated_branch_prior_mean?: when the integrated branch prior is exponential, this is the prior mean.
- integrated_branch_prior_log_mean?: when the integrated branch prior is lognormal, this is the prior log mean.
- integrated_branch_prior_variance?: when the integrated branch prior is lognormal, this is the prior log variance.
- integrated_branch_hyper_prior?: specify whether the integrated branch hyperprior parameters are estimated or fixed.
- prior_expected_parameter_chgpts: prior expected number of parameter changepoints
- tau_prior: choice of prior distribution on the topologies along the alignment
- tau_dim_prior: choice of prior distribution on the number of topology changepoints
- monophyly_probability: the prior probability of monophyly throughout the alignment under the
**monophyly**prior - single_event_probability: the prior probability of a single recombination event at a shared inter-genotype topology changepoint
- prior_expected_cops: the prior expected number of topology changepoints (recombination points)
- prior_expected_ancestry_cops: the prior expected number of topology change points where the ancestry of at least one query changes
- prior_expected_split_ancestry_cops: the prior expected number of topology change points where the ancestry of at least one query changes
*and*bordered by a split ancestry topology on the left or right, but not both sides. - prior_expected_other_cops: the prior expected number of topology change points not falling in other categories
- lambda?: the prior expected number of change points under the single changepoint model

- Controlling cBrother proposal distributions
- hky_kappa_proposal: the proposal distribution for the transition/transversion ratio
- hky_kappa_proposal_sd?: the standard deviation of the normal proposal distribution for transition/transversion ratio
- hky_kappa_proposal_tuner?: the tuning parameter for the "exponential" proposal distribution for transition/transversion ratio
- integrated_branch_proposal_tuner?: the tuning parameter for the "exponential" proposal distribution for integrated branch length
- window_length: for updating changepoints, new locations are proposed uniformly within a window of this size centered on the current changepoint location
- sigma_alpha: the standard deviation of the perturbation of transition/transversion ratios from the current transition/transversion ratio when proposing a new parameter changepoint
- sigma_mu: the standard deviation of the perturbation of integrated branch lengths from the current integrated branch length when proposing a new parameter changepoint
- reversible_jump_probability: tuning parameter for move probabilities; less time is dedicated to trans-dimensional moves as this number drops
- tau_update: set the type of proposal distribution used for updating topologies
- same_ancestry_probability: probability of proposing a new topology with the same ancestry as the existing topology
- same_morphology_probability: probability of proposing a new topology with the same morphology (monophyly/polyphyly) as the existing topology
- split_ancestry_topology: probability of proposing a split topology when proposing a new topology

- Controlling the initial state of the cBrother sampler
- initial_hky_kappa: starting transition/transversion ratio
- initial_hky_kappa_max: when using a uniform initial distribution for transition/transversion ratio, this is the maximum
- initial_integrated_branch: starting value for the integrated branch

- Simulating data with cBrother: there are many options for simulating data according to the cBrother models, but there is no documentation yet
- Obscure commands you don't want to use. I'm warning you!!
- compute_likelihood: compute the likelihood during MCMC
- random: choose the random number generator

- Controlling how cBrother runs: Use these commands to set the properties of the MCMC run.
- Command Line Options: if links are not included, the description here should suffice
- --continue: set to continue a previous MCMC run
- --length: set the length of the MCMC run
- --burnin: set the length of the MCMC burnin
- --subsample: set the subsample rate for the MCMC run
- --quiet?: no superfluous output
- --dont_run?: don't actually run, just parse the command line and simulate or read the alignment data.

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