NAME

       ClonalFrameML - Efficient Inference of Recombination in Whole Bacterial Genomes

SYNOPSIS

       ClonalFrameML newick_file fasta_file output_file [OPTIONS]

DESCRIPTION

       ClonalFrameML  is  a  software  package  that  performs efficient inference of recombination in bacterial
       genomes. ClonalFrameML was created by Xavier Didelot and Daniel Wilson. ClonalFrameML can be  applied  to
       any  type  of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is
       able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. There  are
       three  main outputs from a run of ClonalFrameML: a phylogeny with branch lengths corrected to account for
       recombination, an estimation of the key parameters of the recombination process, and  a  genomic  map  of
       where recombination took place for each branch of the phylogeny.

       ClonalFrameML  is  a  maximum  likelihood  implementation  of the Bayesian software ClonalFrame which was
       previously described by Didelot and Falush (2007). The recombination model underpinning ClonalFrameML  is
       exactly  the  same  as for ClonalFrame, but this new implementation is a lot faster, is able to deal with
       much larger genomic dataset, and does not suffer from MCMC convergence issues

OPTIONS

   Options specifying the analysis type
       -em    true (default) or false   Estimate parameters by a Baum-Welch expectation maximization algorithm.

       -embranch
              true or false (default)   Estimate parameters for each branch using the EM algorithm.

       -rescale_no_recombination
              true or false (default)   Rescale branch lengths for given sites with no recombination model.

       -imputation_only
              true or false (default)   Perform only ancestral state reconstruction and imputation.

   Options affecting all analyses
       -kappa value > 0 (default 2.0)   Relative rate of transitions vs transversions in substitution model

       -fasta_file_list
              true or false (default)   Take fasta_file to be a white-space separated file list.

       -xmfa_file
              true or false (default)   Take fasta_file to be an XMFA file.

       -ignore_user_sites
              sites_file                Ignore sites listed in whitespace-separated sites_file.

       -ignore_incomplete_sites
              true or false (default)   Ignore sites with any ambiguous bases.

       -use_incompatible_sites
              true (default) or false   Use homoplasious and multiallelic sites to correct branch lengths.

       -show_progress
              true or false (default)   Output the progress of the maximum likelihood routines.

       -chromosome_name
              name, eg "chr"            Output importation status file in  BED  format  using  given  chromosome
              name.

       -min_branch_length
              value > 0 (default 1e-7)  Minimum branch length.

       -reconstruct_invariant_sites
              true or false (default)   Reconstruct the ancestral states at invariant sites.

       -label_uncorrected_tree
              true or false (default)   Regurgitate the uncorrected Newick tree with internal nodes labelled.

   Options affecting -em and -embranch:
       -prior_mean
              df "0.1 0.001 0.1 0.0001" Prior mean for R/theta, 1/delta, nu and M.

       -prior_sd
              df "0.1 0.001 0.1 0.0001" Prior standard deviation for R/theta, 1/delta, nu and M.

       -initial_values
              default "0.1 0.001 0.05"  Initial values for R/theta, 1/delta and nu.

       -guess_initial_m
              true (default) or false   Initialize M and nu jointly in the EM algorithms.

       -emsim value >= 0  (default 0)   Number of simulations to estimate uncertainty in the EM results.

       -embranch_dispersion
              value > 0 (default .01)   Dispersion in parameters among branches in the -embranch model.

   Options affecting -rescale_no_recombination:
       -brent_tolerance
              tolerance (default .001)  Set the tolerance of the Brent routine for -rescale_no_recombination.

       -powell_tolerance
              tolerance (default .001)  Set the tolerance of the Powell routine for -rescale_no_recombination.

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.