ClonalFrameML(1) on Linux
The text f560e821dcf7, as Debian 13 (Trixie), Debian 12 (Bookworm), Debian 11 (Bullseye), Debian 10 (Buster) shipped it. The page shows this text now.
Efficient Inference of Recombination in Whole Bacterial Genomes
Flags it lists
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-brent_tolerance -
-chromosome_name -
-em -
-embranch -
-embranch_dispersion -
-emsim -
-fasta_file_list -
-guess_initial_m -
-ignore_incomplete_sites -
-ignore_user_sites -
-imputation_only -
-initial_values -
-kappa -
-label_uncorrected_tree -
-min_branch_length -
-powell_tolerance -
-prior_mean -
-prior_sd -
-reconstruct_invariant_sites -
-rescale_no_recombination -
-show_progress -
-use_incompatible_sites -
-xmfa_file