Provided by: clonalframeml_1.11-1_amd64 bug


       ClonalFrameML - Efficient Inference of Recombination in Whole Bacterial Genomes


       ClonalFrameML newick_file fasta_file output_file [OPTIONS]


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

              true  or  false  (default)    Estimate  parameters  for  each  branch  using the EM

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

              true   or  false  (default)    Perform  only  ancestral  state  reconstruction  and

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

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

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

              sites_file                Ignore sites listed in whitespace-separated sites_file.

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

              true (default) or false   Use homoplasious and multiallelic sites to correct branch

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

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

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

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

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

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

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

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

              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

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

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

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


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