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.
