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.