.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH PPLACER "1" "June 2020" "pplacer 1.1~alpha19" "User Commands"
.SH NAME
pplacer \- place reads on a phylogenetic tree
.SH SYNOPSIS
.B pplacer
[options] [alignment]
.SH OPTIONS
.TP
\fB\-c\fR
Specify the path to the reference package.
.TP
\fB\-t\fR
Specify the reference tree filename.
.TP
\fB\-r\fR
Specify the reference alignment filename.
.TP
\fB\-s\fR
Supply a phyml stats.txt or a RAxML info file giving the model parameters.
.TP
\fB\-d\fR
Specify the directory containing the reference information.
.TP
\fB\-p\fR
Calculate posterior probabilities.
.TP
\fB\-m\fR
Substitution model. Protein: LG, WAG, or JTT. Nucleotides: GTR.
.TP
\fB\-\-model\-freqs\fR
Use model frequencies instead of reference alignment frequencies.
.TP
\fB\-\-gamma\-cats\fR
Number of categories for discrete gamma model.
.TP
\fB\-\-gamma\-alpha\fR
Specify the shape parameter for a discrete gamma model.
.TP
\fB\-\-ml\-tolerance\fR
1st stage branch len optimization tolerance (2nd stage to 1e\-5). Default: 0.01.
.TP
\fB\-\-pp\-rel\-err\fR
Relative error for the posterior probability calculation. Default is 0.01.
.TP
\fB\-\-unif\-prior\fR
Use a uniform prior rather than exponential.
.TP
\fB\-\-inform\-prior\fR
Use an informative exponential prior based on rooted distance to leaves.
.TP
\fB\-\-prior\-lower\fR
Lower bound for the informative prior mean. Default is 0.
.TP
\fB\-\-start\-pend\fR
Starting pendant branch length. Default is 0.1.
.TP
\fB\-\-max\-pend\fR
Set the maximum ML pendant branch length. Default is 2.
.TP
\fB\-\-fig\-cutoff\fR
The cutoff for determining figs. Default is 0; specify 0 to disable.
.TP
\fB\-\-fig\-eval\-all\fR
Evaluate all likelihoods to ensure that the best location was selected.
.TP
\fB\-\-fig\-eval\-discrepancy\-tree\fR
Write out a tree showing the discrepancies between the best complete and observed locations.
.TP
\fB\-\-fig\-tree\fR
Write out a tree showing the figs on the tree.
.TP
\fB\-\-max\-strikes\fR
Maximum number of strikes for baseball. 0 \-> no ball playing. Default is 6.
.TP
\fB\-\-strike\-box\fR
Set the size of the strike box in log likelihood units. Default is 3.
.TP
\fB\-\-max\-pitches\fR
Set the maximum number of pitches for baseball. Default is 40.
.TP
\fB\-\-fantasy\fR
Desired likelihood cutoff for fantasy baseball mode. 0 \-> no fantasy.
.TP
\fB\-\-fantasy\-frac\fR
Fraction of fragments to use when running fantasy baseball. Default is 0.1.
.TP
\fB\-\-write\-masked\fR
Write alignment masked to the region without gaps in the query.
.TP
\fB\-\-verbosity\fR
Set verbosity level. 0 is silent, and 2 is quite a lot. Default is 1.
.TP
\fB\-\-out\-dir\fR
Specify the directory to write place files to.
.TP
\fB\-o\fR
Specify the output file name
.TP
\fB\-\-pretend\fR
Only check out the files then report. Do not run the analysis.
.TP
\fB\-\-check\-like\fR
Write out the likelihood of the reference tree, calculated two ways.
.TP
\fB\-j\fR
The number of child processes to spawn when doing placements. Default is 2.
.TP
\fB\-\-timing\fR
Display timing information after the pplacer run finishes.
.TP
\fB\-\-no\-pre\-mask\fR
Don't pre\-mask sequences before placement.
.TP
\fB\-\-write\-pre\-masked\fR
Write out the pre\-masked sequences to the specified fasta file before placement.
.TP
\fB\-\-map\-mrca\fR
Specify a file to write out MAP sequences for MRCAs and corresponding placements.
.TP
\fB\-\-map\-mrca\-min\fR
Specify cutoff for inclusion in MAP sequence file. Default is 0.8.
.TP
\fB\-\-map\-identity\fR
Add the percent identity of the query sequence to the nearest MAP sequence to each placement.
.TP
\fB\-\-keep\-at\-most\fR
The maximum number of placements we keep. Default is 7.
.TP
\fB\-\-keep\-factor\fR
Throw away anything that has ml_ratio below keep_factor times (best ml_ratio). Default is 0.01.
.TP
\fB\-\-mrca\-class\fR
Classify with MRCAs instead of a painted tree.
.TP
\fB\-\-groups\fR
Split query alignment into the specified number of groups.
.TP
\fB\-\-always\-refine\fR
Always refine the model before placing.
.TP
\fB\-\-mmap\-file\fR
Instead of doing large allocations, mmap the given file. It will be created if it doesn't exist.
.TP
\fB\-\-discard\-nonoverlapped\fR
When pre\-masking, silently discard sequences which don't overlap the mask.
.TP
\fB\-\-version\fR
Write out the version number and exit.
.TP
\fB\-help\fR
Display this list of options
.TP
\fB\-\-help\fR
Display this list of options
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.