Perform multiple sequence alignment on all the fasta files
saved in a given folder. Alignment is conducted using
"BiocManager::install("DECIPHER")". Note that this function first
optimizes the direction of the sequences, then aligns
using "BDECIPHER", and finally masks the resulting
alignment (optionally but does it per default). The
masking step includes removing common gaps across all the species and removing
highly ambiguous positions. The resulting aligned sequences
are stored to a new folder
"2.Alignments".'
Usage
sq.aln(
folder = "1.CuratedSequences",
FilePatterns = "renamed",
sqs.object = NULL,
mask = TRUE,
maxFractionGapsSpecies = 0.01,
...
)Arguments
- folder
Name of the folder where the sequences to align are stored (character).
- FilePatterns
A string that is common to all the target files in the relevant folder (character). Note that this argument can be set to
"NULL"if no specific pattern wants to be analyzed.- sqs.object
A list of sequences generated from sq.curate. Only use if you're not interested in download sequences locally.
- mask
Removes ambiguous sites (Logical, TRUE or FALSE).
- maxFractionGapsSpecies
Maximum fraction of gaps per species (when masked)
- ...
Arguments passed to
"DECIPHER::AlignSeqs".
Value
This function will return an object of class list including the
original and renamed sequence alignments. Optionally, this object will
also include the masked alignments.
Examples
if (FALSE) {
sq.retrieve.direct(
clades = c("Felis", "Vulpes", "Phoca"),
species = "Manis_pentadactyla",
genes = c("ADORA3", "CYTB")
)
sq.curate(
filterTaxonomicCriteria = "Felis|Vulpes|Phoca|Manis",
kingdom = "animals", folder = "0.Sequences"
)
sq.aln(folder = "1.CuratedSequences")
}