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Path	Synopsis
phygeo PhyGeo is a tool for phylogenetic biogeography analysis.	PhyGeo is a tool for phylogenetic biogeography analysis.
diff Package diff is a metapackage for commands that dealt with the biogeographic inference using a diffusion model.	Package diff is a metapackage for commands that dealt with the biogeographic inference using a diffusion model.
diff/freq Package freq implements a command to calculate pixel frequencies from the stochastic mapping output.	Package freq implements a command to calculate pixel frequencies from the stochastic mapping output.
diff/integrate Package integrate implements a numerical integration of the likelihood curve for a diffusion model.	Package integrate implements a numerical integration of the likelihood curve for a diffusion model.
diff/like Package like implements a command to perform a biogeographic reconstruction using likelihood.	Package like implements a command to perform a biogeographic reconstruction using likelihood.
diff/mapcmd Package mapcmd implements a command to draw range reconstructions from pixel probability files.	Package mapcmd implements a command to draw range reconstructions from pixel probability files.
diff/ml Package ml implements a command to search for the maximum likelihood estimation of a biogeographic reconstruction.	Package ml implements a command to search for the maximum likelihood estimation of a biogeographic reconstruction.
diff/particles Package particles implements a command to run a stochastic mapping from a down-pass reconstruction.	Package particles implements a command to run a stochastic mapping from a down-pass reconstruction.
diff/speed Package speed implements a command to measure the speed and distance traveled in a reconstruction.	Package speed implements a command to measure the speed and distance traveled in a reconstruction.
geo Package geo is a metapackage for commands that dealt with paleogeographic reconstruction models.	Package geo is a metapackage for commands that dealt with paleogeographic reconstruction models.
geo/add Package add implements a command to add a paleogeographic reconstruction model to a PhyGeo project.	Package add implements a command to add a paleogeographic reconstruction model to a PhyGeo project.
geo/prior Package prior implements a command to manage pixel priors defined for a project.	Package prior implements a command to manage pixel priors defined for a project.
prj Package prj implements a command to print the basic information of a project.	Package prj implements a command to print the basic information of a project.
rangecmd Package rangecmd is a metapackage for commands that dealt with taxon distribution ranges.	Package rangecmd is a metapackage for commands that dealt with taxon distribution ranges.
rangecmd/add Package add implements a command to add taxon ranges to a PhyGeo project.	Package add implements a command to add taxon ranges to a PhyGeo project.
rangecmd/kde Package kde implements a command to estimate the range distributions using a kernel density estimator.	Package kde implements a command to estimate the range distributions using a kernel density estimator.
rangecmd/mapcmd Package mapcmd implements a command to draw the geographic range of the taxa in a PhyGeo project with defined distribution ranges.	Package mapcmd implements a command to draw the geographic range of the taxa in a PhyGeo project with defined distribution ranges.
rangecmd/remove Package remove implements a command to remove range distribution records not present on a tree.	Package remove implements a command to remove range distribution records not present on a tree.
rangecmd/rotate Package rotate implements a command to rotate the point records of a phygeo project.	Package rotate implements a command to rotate the point records of a phygeo project.
rangecmd/taxa Package terms implements a command to print the list of taxa in a PhyGeo project with defined distribution ranges.	Package terms implements a command to print the list of taxa in a PhyGeo project with defined distribution ranges.
tree Package tree is a metapackage for commands that dealt with phylogenetic trees.	Package tree is a metapackage for commands that dealt with phylogenetic trees.
tree/add Package add implements a command to add trees to a PhyGeo project.	Package add implements a command to add trees to a PhyGeo project.
tree/draw Package draw implements a command to draw trees in a phygeo project as SVG files.	Package draw implements a command to draw trees in a phygeo project as SVG files.
tree/list Package list implements a command to print the list of trees in a phygeo project.	Package list implements a command to print the list of trees in a phygeo project.
tree/remove Package remove implements a command to remove tree terminals from a PhyGeo project without defined distribution ranges.	Package remove implements a command to remove tree terminals from a PhyGeo project without defined distribution ranges.
tree/terms Package terms implements a command to print the list of the terminals in the trees of a PhyGeo project.	Package terms implements a command to print the list of the terminals in the trees of a PhyGeo project.