Provided by: clonalframeml_1.11-1_amd64

**NAME**

ClonalFrameML - Efficient Inference of Recombination in Whole Bacterial Genomes

**SYNOPSIS**

ClonalFrameMLnewick_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**

Optionsspecifyingtheanalysistype-emtrue (default) or false Estimate parameters by a Baum-Welch expectation maximization algorithm.-embranchtrue or false (default) Estimate parameters for each branch using the EM algorithm.-rescale_no_recombinationtrue or false (default) Rescale branch lengths for given sites with no recombination model.-imputation_onlytrue or false (default) Perform only ancestral state reconstruction and imputation.Optionsaffectingallanalyses-kappavalue > 0 (default 2.0) Relative rate of transitions vs transversions in substitution model-fasta_file_listtrue or false (default) Take fasta_file to be a white-space separated file list.-xmfa_filetrue or false (default) Take fasta_file to be an XMFA file.-ignore_user_sitessites_file Ignore sites listed in whitespace-separated sites_file.-ignore_incomplete_sitestrue or false (default) Ignore sites with any ambiguous bases.-use_incompatible_sitestrue (default) or false Use homoplasious and multiallelic sites to correct branch lengths.-show_progresstrue or false (default) Output the progress of the maximum likelihood routines.-chromosome_namename, eg "chr" Output importation status file in BED format using given chromosome name.-min_branch_lengthvalue > 0 (default 1e-7) Minimum branch length.-reconstruct_invariant_sitestrue or false (default) Reconstruct the ancestral states at invariant sites.-label_uncorrected_treetrue or false (default) Regurgitate the uncorrected Newick tree with internal nodes labelled.Optionsaffecting-emand-embranch:-prior_meandf "0.1 0.001 0.1 0.0001" Prior mean for R/theta, 1/delta, nu and M.-prior_sddf "0.1 0.001 0.1 0.0001" Prior standard deviation for R/theta, 1/delta, nu and M.-initial_valuesdefault "0.1 0.001 0.05" Initial values for R/theta, 1/delta and nu.-guess_initial_mtrue (default) or false Initialize M and nu jointly in the EM algorithms.-emsimvalue >= 0 (default 0) Number of simulations to estimate uncertainty in the EM results.-embranch_dispersionvalue > 0 (default .01) Dispersion in parameters among branches in the-embranchmodel.Optionsaffecting-rescale_no_recombination:-brent_tolerancetolerance (default .001) Set the tolerance of the Brent routine for-rescale_no_recombination.-powell_tolerancetolerance (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.