dropSeq: Removes duplicated accessions of the same species in DNA...

In domingoscardoso/catGenes: Concatenating multiple DNA alignments and other phylogenetic features

Removes duplicated accessions of the same species in DNA alignments

Description

This function drops the smaller sequence(s) (with missing characters) for any species duplicated with multiple accessions in the DNA alignment. You can run dropSeq with multiple DNA alignments, but then we recommend to run catmultGenes first.

Usage

dropSeq(...,
        shortaxlabel = FALSE)

Arguments

...	one or a list of NEXUS-formatted gene datasets as loaded by ape's read.nexus.data, for example. You can also load the resulting list of equally-sized dataframes containing the input gene datasets, as generated by the function catmultGenes.
shortaxlabel	Logical, if TRUE the final individual gene dataset will delete the accession numbers associated with each species or sequence.

Value

A list of dataframe(s) containing the input DNA alignment(s), where duplicated accessions of the same species are removed.

Author(s)

Domingos Cardoso

See Also

catmultGenes

writeNexus

writePhylip

nexusdframe

phylipdframe

fastadframe

Examples

## Not run: 
data(Ormosia)

# Run dropSeq for one or more individual DNA alignment and then save each
# dataset with non-duplicated species using nexusdframe, phylipdframe or fastadframe
df <- dropSeq(Ormosia)
ITS <- df[[1]]
nexusdframe(ITS, file = "filename.nex")


# Run function catmultGenes first
catdf <- catmultGenes(Ormosia,
                      maxspp = TRUE,
                      shortaxlabel = FALSE,
                      missdata = TRUE)

# Run dropSeq for the entire concatenated DNA alignments
catdf <- dropSeq(catdf,
                 shortaxlabel = FALSE)

# Then save the concatenated DNA alignment
writeNexus(catdf,
           file = "filename.nex",
           bayesblock = TRUE,
           interleave = TRUE)

## End(Not run)

domingoscardoso/catGenes documentation built on Feb. 6, 2025, 9:01 p.m.