ape: write.nexus – R documentation

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ape

write.nexus

Write Tree File in Nexus Format

Description

This function writes trees in a file with the NEXUS format.

Usage

write.nexus(..., file = "", translate = TRUE)

Arguments

`...`	either (i) a single object of class `"phylo"`, (ii) a series of such objects separated by commas, or (iii) a list containing such objects.
`file`	a file name specified by either a variable of mode character, or a double-quoted string; if `file = ""` (the default) then the tree is written on the standard output connection.
`translate`	a logical, if `TRUE` (the default) a translation of the tip labels is done which are replaced in the parenthetic representation with tokens.

Details

If several trees are given, they must all have the same tip labels.

If among the objects given some are not trees of class "phylo", they are simply skipped and not written in the file.

See write.tree for details on how tip (and node) labels are checked before being printed.

Value

None (invisible ‘NULL’).

Author(s)

Emmanuel Paradis

References

Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590–621.

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24