ape (version 3.0-3)

write.nexus.data: Write Character Data In NEXUS Format

Description

This function writes in a file a list of sequences in the NEXUS format.The names of the vectors of the list are used as taxon names.

Usage

write.nexus.data(x, file, format = "dna", datablock = TRUE,
                 interleaved = TRUE, charsperline = NULL,
                 gap = NULL, missing = NULL)

Value

None (invisible NULL).

Details

If the sequences have no names, then they are given 1, 2, ..., as names in the file.

Sequences must be all of the same length (i.e., aligned).

Default symbols for missing data and gaps can be changed by using the missing and gap commands.

Please see files data.nex and taxacharacters.nex for examples of output formats.

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.

See Also

read.nexus,write.nexus, read.nexus.data

Examples

\dontshow{library(ape)}
## Write interleaved DNA data with 100 characters per line in a DATA block
data("woodmouse")
write.nexus.data(woodmouse, file= "woodmouse.example.nex", interleaved = TRUE, charsperline = 100)
## Write sequential DNA data in TAXA and CHARACTERS blocks
data("cynipids")
write.nexus.data(cynipids, file= "cynipids.example.nex", format = "protein", datablock = FALSE, interleaved = FALSE)
\dontshow{unlink(c("woodmouse.example.nex", "cynipids.example.nex"))}