pplacer - place reads on a phylogenetic tree
pplacer [options] [alignment]
- -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
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.