NAME

       pplacer - place reads on a phylogenetic tree

SYNOPSIS

       pplacer [options] [alignment]

OPTIONS

       -c     Specify the path to the reference package.

       -t     Specify the reference tree filename.

       -r     Specify the reference alignment filename.

       -s     Supply a phyml stats.txt or a RAxML info file giving the model parameters.

       -d     Specify the directory containing the reference information.

       -p     Calculate posterior probabilities.

       -m     Substitution model. Protein: LG, WAG, or JTT. Nucleotides: GTR.

       --model-freqs
              Use model frequencies instead of reference alignment frequencies.

       --gamma-cats
              Number of categories for discrete gamma model.

       --gamma-alpha
              Specify the shape parameter for a discrete gamma model.

       --ml-tolerance
              1st stage branch len optimization tolerance (2nd stage to 1e-5). Default: 0.01.

       --pp-rel-err
              Relative error for the posterior probability calculation. Default is 0.01.

       --unif-prior
              Use a uniform prior rather than exponential.

       --inform-prior
              Use an informative exponential prior based on rooted distance to leaves.

       --prior-lower
              Lower bound for the informative prior mean. Default is 0.

       --start-pend
              Starting pendant branch length. Default is 0.1.

       --max-pend
              Set the maximum ML pendant branch length. Default is 2.

       --fig-cutoff
              The cutoff for determining figs. Default is 0; specify 0 to disable.

       --fig-eval-all
              Evaluate all likelihoods to ensure that the best location was selected.

       --fig-eval-discrepancy-tree
              Write out a tree showing the discrepancies between the best complete and observed locations.

       --fig-tree
              Write out a tree showing the figs on the tree.

       --max-strikes
              Maximum number of strikes for baseball. 0 -> no ball playing. Default is 6.

       --strike-box
              Set the size of the strike box in log likelihood units. Default is 3.

       --max-pitches
              Set the maximum number of pitches for baseball. Default is 40.

       --fantasy
              Desired likelihood cutoff for fantasy baseball mode. 0 -> no fantasy.

       --fantasy-frac
              Fraction of fragments to use when running fantasy baseball. Default is 0.1.

       --write-masked
              Write alignment masked to the region without gaps in the query.

       --verbosity
              Set verbosity level. 0 is silent, and 2 is quite a lot. Default is 1.

       --out-dir
              Specify the directory to write place files to.

       -o     Specify the output file name

       --pretend
              Only check out the files then report. Do not run the analysis.

       --check-like
              Write out the likelihood of the reference tree, calculated two ways.

       -j     The number of child processes to spawn when doing placements. Default is 2.

       --timing
              Display timing information after the pplacer run finishes.

       --no-pre-mask
              Don't pre-mask sequences before placement.

       --write-pre-masked
              Write out the pre-masked sequences to the specified fasta file before placement.

       --map-mrca
              Specify a file to write out MAP sequences for MRCAs and corresponding placements.

       --map-mrca-min
              Specify cutoff for inclusion in MAP sequence file. Default is 0.8.

       --map-identity
              Add the percent identity of the query sequence to the nearest MAP sequence to each placement.

       --keep-at-most
              The maximum number of placements we keep. Default is 7.

       --keep-factor
              Throw away anything that has ml_ratio below keep_factor times (best ml_ratio). Default is 0.01.

       --mrca-class
              Classify with MRCAs instead of a painted tree.

       --groups
              Split query alignment into the specified number of groups.

       --always-refine
              Always refine the model before placing.

       --mmap-file
              Instead of doing large allocations, mmap the given file. It will be created if it doesn't exist.

       --discard-nonoverlapped
              When pre-masking, silently discard sequences which don't overlap the mask.

       --version
              Write out the version number and exit.

       -help  Display this list of options

       --help Display this list of options

AUTHOR

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

pplacer 1.1~alpha19                                 June 2020                                         PPLACER(1)