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.