catfullGenes: Compares gene datasets for combined phylogenetic analysis

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

Compares gene datasets for combined phylogenetic analysis

Description

Compares a list of "n" gene datasets (individual DNA alignments) and makes them with the same number of taxa, ready for combined, multigene phylogenetic analysis. This function only works for DNA alignments where species do not have duplicated sequences. For concatenation when species have multiple accessions, please use catmultGenes.

Usage

catfullGenes(...,
             shortaxlabel = TRUE,
             missdata = TRUE,
             outgroup = NULL,
             verbose = TRUE)

Arguments

...	a list of NEXUS-formatted gene datasets as read by ape's read.nexus.data or at least two individually ape-read objects of NEXUS-formatted gene datasets.
shortaxlabel	Logical, if FALSE the final individual gene dataset will maintain the accession numbers associated with each species or sequence.
missdata	Logical, if FALSE the comparison will exclude any species that lacks a complete sequence for one of the input gene dataset.
outgroup	Provide the outgroup taxa (either one taxon name or a vector of multiple taxon names that are present in all individual gene dataset) if the concatenation is intended to maintain incomplete taxa (taxa missing the sequence for a particular gene).
verbose	Logical, if FALSE, a message showing each step during gene matching search will not be printed in the console in full.

Value

A list of dataframes of the equally-sized gene dataset, where the first column "species" include all taxon names and the second column "sequence" include the DNA sequence for the corresponding taxon.

Author(s)

Domingos Cardoso and Quezia Cavalcante

See Also

writeNexus

writePhylip

nexusdframe

phylipdframe

fastadframe

Examples

## Not run: 
data(Gaya)
catdf <- catfullGenes(Gaya,
                      shortaxlabel = TRUE,
                      missdata = FALSE,
                      outgroup = "Abutilon_costicalyx",
                      verbose = TRUE)

outgrouptaxa <- c("Abutilon_costicalyx", "Abutilon_itatiaie")
catdf <- catfullGenes(Gaya,
                      shortaxlabel = TRUE,
                      missdata = FALSE,
                      outgroup = outgrouptaxa,
                      verbose = TRUE)

## End(Not run)

domingoscardoso/catGenes documentation built on Jan. 5, 2025, 9:40 p.m.