fasta_organizer: Quality check graphics for DNA Barcodes

In carvajalc/BarcoR: Quality Check Graphics for DNA Barcodes

Description

order species/accessions in a fasta file based in a phylogenetic tree.

Usage

fasta_organizer(
  sequence_fasta_file_user = NULL,
  sequence_nexus_file_user = NULL,
  seqinr_seqtype_user = c("DNA", "AA"),
  organizer_user = c("tree", "a_to_z", "z_to_a"),
  tree_file_user = NULL,
  ape_root_tree_user = NULL,
  ape_ladderize_user = TRUE,
  remove_taxa_if_match_pattern_user = NULL,
  file_out_user = NULL,
  out_directory_user = NULL
)

Arguments

sequence_fasta_file_user	A DNA barcodes file in fasta format.
sequence_nexus_file_user	A DNA barcodes file in Nexus format.
seqinr_seqtype_user	Genetic information class. Either DNA ("DNA") or Aminoacid ("AA") option.
organizer_user	Order criterion. order based in a phylogenetic tree ("tree"). Either ascending order ("a_to_z") or descending order ("z_to_a").
tree_file_user	A phylogentic tree file to be used as order criterion.
ape_root_tree_user	Vector. a species names to root the phylogenetic tree.
ape_ladderize_user	Logical. reorganizes the internal structure of the tree based in ladderize function in ape packages.
remove_taxa_if_match_pattern_user	Vector. Species list to be eliminate on phylogenetic tree and DNA barcode file (fasta or nexus)
file_out_user	Character. an optional name to be added to the output file.
out_directory_user	Output directory.

Value

This function return an ordered fasta file and a phylogenetic tree based in functions parameters.

@examples COX1 <-fasta_organizer (sequence_fasta_file_user = NULL, sequence_nexus_file_user = system.file("extdata","COI_aligned_end6.nexus",package="BarcoR"), seqinr_seqtype_user = "DNA", organizer_user = "tree", tree_file_user = system.file("extdata","COI_aligned_end6_newick.tree",package="BarcoR"), ape_root_tree_user = NULL, ape_ladderize_user = TRUE, remove_taxa_if_match_pattern_user = NULL, file_out_user = "COI_ordered", out_directory_user = NULL)

carvajalc/BarcoR documentation built on Dec. 19, 2021, 1:54 p.m.