README
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PhyGeo
PhyGeo is a tool for phylogenetic biogeography analysis.
Authorship and license
Copyright © 2023 J. Salvador Arias jsalarias@gmail.com. All rights reserved. Distributed under BSD2 licenses that can be found in the LICENSE file.
Directories
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| Path | Synopsis |
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cmd
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phygeo
PhyGeo is a tool for phylogenetic biogeography analysis.
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PhyGeo is a tool for phylogenetic biogeography analysis. |
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phygeo/diff
Package diff is a metapackage for commands that dealt with the biogeographic inference using a diffusion model.
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Package diff is a metapackage for commands that dealt with the biogeographic inference using a diffusion model. |
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phygeo/diff/integrate
Package integrate implements a numerical integration of the likelihood curve for a diffusion model.
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Package integrate implements a numerical integration of the likelihood curve for a diffusion model. |
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phygeo/diff/like
Package like implements a command to perform a biogeographic reconstruction using likelihood.
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Package like implements a command to perform a biogeographic reconstruction using likelihood. |
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phygeo/diff/mapcmd
Package mapcmd implements a command to draw the range reconstructions of a tree nodes.
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Package mapcmd implements a command to draw the range reconstructions of a tree nodes. |
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phygeo/diff/ml
Package ml implements a command to search for the maximum likelihood estimation of a biogeographic reconstruction.
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Package ml implements a command to search for the maximum likelihood estimation of a biogeographic reconstruction. |
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phygeo/diff/speed
Package speed implements a command to measure the speed and distance traveled in a reconstruction.
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Package speed implements a command to measure the speed and distance traveled in a reconstruction. |
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phygeo/geo
Package geo is a metapackage for commands that dealt with paleogeographic reconstruction models.
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Package geo is a metapackage for commands that dealt with paleogeographic reconstruction models. |
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phygeo/geo/add
Package add implements a command to add a paleogeographic reconstruction model to a PhyGeo project.
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Package add implements a command to add a paleogeographic reconstruction model to a PhyGeo project. |
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phygeo/geo/prior
Package prior implements a command to manage pixel priors defined for a project.
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Package prior implements a command to manage pixel priors defined for a project. |
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phygeo/rangecmd
Package rangecmd is a metapackage for commands that dealt with taxon distribution ranges.
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Package rangecmd is a metapackage for commands that dealt with taxon distribution ranges. |
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phygeo/rangecmd/add
Package add implements a command to add taxon ranges to a PhyGeo project.
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Package add implements a command to add taxon ranges to a PhyGeo project. |
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phygeo/rangecmd/taxa
Package terms implements a command to print the list of taxa in a PhyGeo project with defined distribution ranges.
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Package terms implements a command to print the list of taxa in a PhyGeo project with defined distribution ranges. |
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phygeo/tree
Package tree is a metapackage for commands that dealt with phylogenetic trees.
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Package tree is a metapackage for commands that dealt with phylogenetic trees. |
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phygeo/tree/add
Package add implements a command to add trees to a PhyGeo project.
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Package add implements a command to add trees to a PhyGeo project. |
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phygeo/tree/list
Package list implements a command to print the list of trees in a phygeo project.
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Package list implements a command to print the list of trees in a phygeo project. |
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phygeo/tree/terms
Package terms implements a command to print the list of the terminals in the trees of a PhyGeo project.
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Package terms implements a command to print the list of the terminals in the trees of a PhyGeo project. |
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infer
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diffusion
Package diffusion implements an spherical diffusion approximated using a discrete isolatitude pixelation for a phylogenetic biogeography analysis.
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Package diffusion implements an spherical diffusion approximated using a discrete isolatitude pixelation for a phylogenetic biogeography analysis. |
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Package project implements reading and writing of PhyGeo project files.
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Package project implements reading and writing of PhyGeo project files. |
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