alignSequences: Align sequences in a seqlist

In thebustalab/phylochemistry: Chemical and Sequence Analyses in a Phylogenetic Context

Description

Align sequences in a seqlist

Usage

alignSequences(
  monolist,
  subset,
  alignment_directory_path,
  sequences_of_interest_directory_path,
  input_sequence_type = c("nucl", "amin"),
  mode = c("nucl_align", "amin_align", "codon_align", "fragment_align"),
  base_fragment = NULL
)

Arguments

monolist	Monolist of the sequences to be aligned. First column should be "accession"
subset	TRUE/FALSE column in monolist that specifies which sequences should be included in the alignment
alignment_directory_path	Path to where the alignment should be written
sequences_of_interest_directory_path	Path to a directory where blast hits should be written out as fasta files
input_sequence_type	One of "nucl" or "amin"
mode	One of "nucl_align", "amin_align", or "codon_align"
base_fragment	TROUBLESHOOTING: "ERROR: inconsistency between the following pep and nuc seqs" - usually means there are duplicate accessions numbers in the input monolist

thebustalab/phylochemistry documentation built on Sept. 3, 2021, 5:06 a.m.