[med-svn] [clonalframeml] 01/02: Add manpage

[Andreas Tille]

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commit ecc4de1ab17afa4130f25f6ec11e23e8f0d9ce90
Author: Andreas Tille <tille at debian.org>
Date:   Thu Sep 21 11:01:54 2017 +0200

    Add manpage
---
 debian/ClonalFrameML.1 | 100 +++++++++++++++++++++++++++++++++++++++++++++++++
 debian/manpages        |   1 +
 2 files changed, 101 insertions(+)

diff --git a/debian/ClonalFrameML.1 b/debian/ClonalFrameML.1
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index 0000000..363165c
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+.TH CLONALFRAMEML "1" "September 2017" "ClonalFrameML 1.11" "User Commands"
+.SH NAME
+ClonalFrameML \- Efficient Inference of Recombination in Whole Bacterial Genomes
+.SH SYNOPSIS
+.B ClonalFrameML
+newick_file fasta_file output_file \fB[OPTIONS]\fR
+.SH 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.
+.PP
+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
+.SH OPTIONS
+.SS Options specifying the analysis type
+.TP
+\fB\-em\fR
+true (default) or false   Estimate parameters by a Baum\-Welch expectation maximization algorithm.
+.TP
+\fB\-embranch\fR
+true or false (default)   Estimate parameters for each branch using the EM algorithm.
+.TP
+\fB\-rescale_no_recombination\fR
+true or false (default)   Rescale branch lengths for given sites with no recombination model.
+.TP
+\fB\-imputation_only\fR
+true or false (default)   Perform only ancestral state reconstruction and imputation.
+.SS Options affecting all analyses
+.TP
+\fB\-kappa\fR
+value > 0 (default 2.0)   Relative rate of transitions vs transversions in substitution model
+.TP
+\fB\-fasta_file_list\fR
+true or false (default)   Take fasta_file to be a white\-space separated file list.
+.TP
+\fB\-xmfa_file\fR
+true or false (default)   Take fasta_file to be an XMFA file.
+.TP
+\fB\-ignore_user_sites\fR
+sites_file                Ignore sites listed in whitespace\-separated sites_file.
+.TP
+\fB\-ignore_incomplete_sites\fR
+true or false (default)   Ignore sites with any ambiguous bases.
+.TP
+\fB\-use_incompatible_sites\fR
+true (default) or false   Use homoplasious and multiallelic sites to correct branch lengths.
+.TP
+\fB\-show_progress\fR
+true or false (default)   Output the progress of the maximum likelihood routines.
+.TP
+\fB\-chromosome_name\fR
+name, eg "chr"            Output importation status file in BED format using given chromosome name.
+.TP
+\fB\-min_branch_length\fR
+value > 0 (default 1e\-7)  Minimum branch length.
+.TP
+\fB\-reconstruct_invariant_sites\fR
+true or false (default)   Reconstruct the ancestral states at invariant sites.
+.TP
+\fB\-label_uncorrected_tree\fR
+true or false (default)   Regurgitate the uncorrected Newick tree with internal nodes labelled.
+.SS Options affecting \fB\-em\fR and \fB\-embranch\fR:
+.TP
+\fB\-prior_mean\fR
+df "0.1 0.001 0.1 0.0001" Prior mean for R/theta, 1/delta, nu and M.
+.TP
+\fB\-prior_sd\fR
+df "0.1 0.001 0.1 0.0001" Prior standard deviation for R/theta, 1/delta, nu and M.
+.TP
+\fB\-initial_values\fR
+default "0.1 0.001 0.05"  Initial values for R/theta, 1/delta and nu.
+.TP
+\fB\-guess_initial_m\fR
+true (default) or false   Initialize M and nu jointly in the EM algorithms.
+.TP
+\fB\-emsim\fR
+value >= 0  (default 0)   Number of simulations to estimate uncertainty in the EM results.
+.TP
+\fB\-embranch_dispersion\fR
+value > 0 (default .01)   Dispersion in parameters among branches in the \fB\-embranch\fR model.
+.SS Options affecting \fB\-rescale_no_recombination\fR:
+.TP
+\fB\-brent_tolerance\fR
+tolerance (default .001)  Set the tolerance of the Brent routine for \fB\-rescale_no_recombination\fR.
+.TP
+\fB\-powell_tolerance\fR
+tolerance (default .001)  Set the tolerance of the Powell routine for \fB\-rescale_no_recombination\fR.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/manpages b/debian/manpages
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index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1

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