I have been using the R phangorn package to open a fasta file into phyDat format to analyze.
I believe I have set up the file reading incorrectly:
dataFile <- file("primatesAA.meg")
phyData <- read.phyDat(dataFile, format = "fasta", type = "AA")
modelTest(dataFile, tree = NULL, model = "all", G = TRUE, I = TRUE,
FREQ = FALSE, k = 4, control = pml.control(epsilon = 1e-08, maxit = 10,
trace = 1), multicore = FALSE, mc.cores
= NULL)
I got the following error message.
dataFile <- file("primatesAA.meg") phyData <- read.phyDat(dataFile, format = "fasta", type = "AA") Error in if (ncol(data) == 1) compress <- FALSE : argument is of length zero In addition: Warning message: In read.FASTA(file, type = "AA") : failed to read sequences, returns NULL
Is there a correct way to set this up?