CLONALFRAMEML(1)

Okay bestie, come sit with me, because CLONALFRAMEML(1) is giving User Commands energy and I need you to see it 💅🫶

✨ NAME ✨

ClonalFrameML is all about Efficient Inference of Recombination in Whole Bacterial Genomes 🦋

🎀 SYNOPSIS 🎀

ClonalFrameML newick_file fasta_file output_file [OPTIONS]

🌸 DESCRIPTION 🌸

Okay so ClonalFrameML is a software package that does efficient inference of recombination in bacterial genomes, and it is literally so good 😭 It was created by Xavier Didelot and Daniel Wilson. It works on any type of aligned sequence data, but it's especially made for whole genome sequences. It can compare hundreds of whole genomes in a matter of hours on a standard Desktop computer, which is giving main character energy 👑

A run of ClonalFrameML gives you three main outputs 🧁. First, a phylogeny with branch lengths corrected to account for recombination. Second, an estimation of the key parameters of the recombination process. Third, a genomic map of where recombination took place for each branch of the phylogeny.

ngl the lineage is iconic. ClonalFrameML is a maximum likelihood implementation of the Bayesian software ClonalFrame, which was previously described by Didelot and Falush (2007) 🌈 The recombination model underneath ClonalFrameML is exactly the same as ClonalFrame's, but this new version is a lot faster, can handle way bigger genomic datasets, and does not suffer from MCMC convergence issues. No more convergence drama 💖

🌈 OPTIONS 🌈

🧪 Options specifying the analysis type

• -em — Takes true (default) or false. Estimates parameters with a Baum-Welch expectation maximization algorithm.
• -embranch — Takes true or false (default). Estimates parameters for each branch using the EM algorithm.
• -rescale_no_recombination — Takes true or false (default). Rescales branch lengths for given sites with no recombination model.
• -imputation_only — Takes true or false (default). Only does ancestral state reconstruction and imputation, nothing extra 🙈

🍓 Options affecting all analyses

• -kappa — Takes value > 0 (default 2.0). This is the relative rate of transitions vs transversions in the substitution model ✨
• -fasta_file_list — Takes true or false (default). Treats fasta_file as a white-space separated file list 📝
• -xmfa_file — Takes true or false (default). Treats fasta_file as an XMFA file.
• -ignore_user_sites — Takes sites_file. Ignores the sites listed in the whitespace-separated sites_file 🫧
• -ignore_incomplete_sites — Takes true or false (default). Ignores sites with any ambiguous bases.
• -use_incompatible_sites — Takes true (default) or false. Uses homoplasious and multiallelic sites to correct branch lengths 🔥
• -show_progress — Takes true or false (default). Outputs the progress of the maximum likelihood routines, so you can watch the magic happen 👀
• -chromosome_name — Takes a name, eg "chr". Outputs the importation status file in BED format using the chromosome name you give it 🧬
• -min_branch_length — Takes value > 0 (default 1e-7). Sets the minimum branch length 💜
• -reconstruct_invariant_sites — Takes true or false (default). Reconstructs the ancestral states at invariant sites.
• -label_uncorrected_tree — Takes true or false (default). Spits out the uncorrected Newick tree with the internal nodes labelled 🌸

🎀 Options affecting -em and -embranch

• -prior_mean — Takes df "0.1 0.001 0.1 0.0001" as the default. Sets the prior mean for R/theta, 1/delta, nu and M 🍭
• -prior_sd — Takes df "0.1 0.001 0.1 0.0001" as the default. Sets the prior standard deviation for R/theta, 1/delta, nu and M.
• -initial_values — Takes default "0.1 0.001 0.05". Sets the initial values for R/theta, 1/delta and nu 🌷
• -guess_initial_m — Takes true (default) or false. Initializes M and nu jointly in the EM algorithms 🧚
• -emsim — Takes value >= 0 (default 0). The number of simulations used to estimate uncertainty in the EM results.
• -embranch_dispersion — Takes value > 0 (default .01). The dispersion in parameters among branches in the -embranch model 🦋

💅 Options affecting -rescale_no_recombination

• -brent_tolerance — Takes a tolerance (default .001). Sets the tolerance of the Brent routine for -rescale_no_recombination 💖
• -powell_tolerance — Takes a tolerance (default .001). Sets the tolerance of the Powell routine for -rescale_no_recombination 🌈

🫶 AUTHOR 🫶

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

That's the tea 🍵 ClonalFrameML 1.11 from September 2017, all wrapped up with CLONALFRAMEML(1) 💜✨