write.nexus

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.

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.

file

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.

translate


  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, MAFFT) whose results are returned into R.

write.nexus: Write Tree File in Nexus Format

Description

Usage

Arguments

Value

Details

References

See Also