View source: R/public_functions.R
Align sequences in a seqlist
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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" TROUBLESHOOTING: "ERROR: inconsistency between the following pep and nuc seqs" - usually means there are duplicate accessions numbers in the input monolist |
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