add

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Published: Aug 28, 2024 License: BSD-2-Clause Imports: 6 Imported by: 0

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Overview

Package add implements a command to add a new taxon to a tree.

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Constants

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Variables

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var Command = &command.Command{
	Usage: `add [-o|--output <file>]
	--tree <tree> --branch <number> --sister <id>
	<taxon-name> <age> [<treefile>]`,
	Short: "add a new taxon to a tree",
	Long: `
Command add adds a new taxon, with a given age, as a sister of the indicated
node.

The first argument of the command is the name of the taxon, if the name has
multiple words, enclosed it in quotations, for example: "Homo sapiens".

The second argument is the age to be given to the taxon, in million years.

The name of a tree file can be given as a third argument. If no file is given
it will read the tree collection from the standard input.

The flag --tree is required and indicates the name of the tree to be modified.

The flag --brLen is required and indicates the branch length, in million
years, of the branch that end at the added taxon.

The flag --sister is required and is the ID of the node that will be the
sister of the added node.

The resulting tree will be printed as a tree file in the standard output. Use
the flag --output, or -o, to define an output file. As this command modifies
the tree, it is possible that node IDs will be modified in the process.
	`,
	SetFlags: setFlags,
	Run:      run,
}

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Types

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