convertAlign | R Documentation |
Convert one or multiple DNA alignments in FASTA, NEXUS or PHYLIP format into each other.
convertAlign(filepath = NULL,
format = NULL,
rmfiles = FALSE,
dir = NULL)
filepath |
Path to the directory where the DNA alignments are stored. |
format |
Define either "NEXUS", "FASTA" or "PHYLIP" format for writing the resulting newly converted files. |
rmfiles |
Logical, if |
dir |
The path to the directory where the newly converted files should be saved. If no directory is given, then the files will saved in a subfolder named after the current date under the folder named RESULTS_convertAlign. |
Domingos Cardoso
## Not run:
library(catGenes)
data(GenBank_accessions)
todaydate <- format(Sys.time(), "%d%b%Y")
folder_mined_seqs <- paste0("RESULTS_mineSeq/", todaydate)
folder_aligned_seqs <- paste0("RESULTS_alignSeqs/", todaydate)
mineSeq(inputdf = GenBank_accessions,
gb.colnames = c("ITS", "matK"),
as.character = FALSE,
verbose = TRUE,
save = TRUE,
dir = "RESULTS_mineSeq",
filename = "GenBanK_seqs")
alignSeqs(filepath = folder_mined_seqs,
method = "ClustalW",
gapOpening = "default",
format = "NEXUS",
verbose = TRUE,
dir = "RESULTS_alignSeqs")
convertAlign(filepath = folder_aligned_seqs,
format = "PHILIP",
rmfiles = FALSE)
## End(Not run)
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