write.nexus

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

manip

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

Simon Blomberg

Ben Bolker

Joseph Brown

Santiago Claramunt

Julien Claude

Hoa Sien Cuong

Richard Desper

Gilles Didier

Benoit Durand

Julien Dutheil

RJ Ewing

Olivier Gascuel

Thomas Guillerme

Christoph Heibl

Anthony Ives

Bradley Jones

Franz Krah

Daniel Lawson

Vincent Lefort

Pierre Legendre

Jim Lemon

Guillaume Louvel

Eric Marcon

Rosemary McCloskey

Johan Nylander

Rainer Opgen-Rhein

Andrei-Alin Popescu

Manuela Royer-Carenzi

Klaus Schliep

Korbinian Strimmer

Damien de Vienne

write.nexus function

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

Arguments

Author

Write Tree File in Nexus Format — write.nexus

<dl>

 <dt>...</dt>
<dd>either (i) a single object of class <code>"phylo"</code>, (ii) a
 series of such objects separated by commas, or (iii) a list
 containing such objects.</dd>

 <dt>file</dt>
<dd>a file name specified by either a variable of mode character,
 or a double-quoted string; if <code>file = ""</code> (the default) then the
 tree is written on the standard output connection.</dd>

 <dt>translate</dt>
<dd>a logical, if <code>TRUE</code> (the default) a translation
 of the tip labels is done which are replaced in the parenthetic
 representation with tokens.</dd>

</dl>

Write Tree File in Nexus Format

write.nexus: Write Tree File in Nexus Format

Description

Usage

Value

Arguments

Author

Details

References

See Also