Commands

Every command prints its options with -h, e.g. gplace place -h.

Command	What it is for
Placing genomes
place	Place the genomes of one alignment on one reference package.
place_batch	Place many alignments at once, each reference package’s alignments together.
compare	Compare two jplace files, e.g. gPlace’s with pplacer’s.
pplacer tools, without installing pplacer
tog	Make a tree with your genomes added at their placements (guppy tog).
taxit	Build or check a reference package (taxtastic’s taxit create, check, info).
Setting up and checking
check_install	Check that gPlace computes exactly as pplacer on this computer.
test	Place bundled genomes and compare them with pplacer’s output.
benchmark	Find the fastest --cpus and estimate a job’s memory and time.
build_engine	Rebuild the compiled engine without reinstalling (advanced).