Analysis Choose an analysis type. Recombination detection, common rates (recommended) Recombination detection, individual rates per-branch Imputation only Rescale the phylogeny without recombination detection next ➡ Files Enter the filename of the Newick-format phylogeny. Enter the filename of one the following: FASTA file representing alignment Text list of FASTA files XMFA file Enter a prefix for the output files. Absolute file locations: I have manually specified full paths preceding filenames All files reside in the following directory: ClonalFrameML executable: I can run the program just by typing "ClonalFrameML" I will run ClonalFrameML from its home directory ClonalFrameML resides in the following directory: ⬅ prev next ➡ Parameters Enter the relative rate of transitions versus transversions (kappa). Prior means R/theta 1/delta nu M Prior standard deviations R/theta 1/delta nu M Initial values R/theta 1/delta nu Initialize M and nu jointly in the EM algorithms Number of simulations to estimate uncertainty in the EM results Dispersion in parameters among branches in the -embranch model ⬅ prev next ➡ Advanced Ignore user sites Ignore sites with any ambiguous bases Use homoplasious and multiallelic sites to correct branch lengths Output the progress of the maximum likelihood routines Minimum branch length Reconstruct the ancestral states at invariant sites Regurgitate the uncorrected Newick tree with internal nodes labelled Tolerance of the Brent routine Tolerance of the Powell routine ⬅ prev