augur align

Align multiple sequences from FASTA.

usage: augur align [-h] --sequences FASTA [FASTA ...] [--output OUTPUT]
                   [--nthreads NTHREADS] [--method {mafft}]
                   [--reference-name NAME] [--reference-sequence PATH]
                   [--remove-reference] [--fill-gaps]
                   [--existing-alignment FASTA] [--debug]

Named Arguments

--sequences, -s

sequences to align

--output, -o

output file (default: “alignment.fasta”)

Default: “alignment.fasta”


number of threads to use; specifying the value ‘auto’ will cause the number of available CPU cores on your system, if determinable, to be used

Default: 1


Possible choices: mafft

alignment program to use

Default: “mafft”


strip insertions relative to reference sequence; use if the reference is already in the input sequences


Add this reference sequence to the dataset & strip insertions relative to this. Use if the reference is NOT already in the input sequences


remove reference sequence from the alignment

Default: False


If gaps represent missing data rather than true indels, replace by N after aligning.

Default: False


An existing alignment to which the sequences will be added. The ouput alignment will be the same length as this existing alignment.

Default: False


Produce extra files (e.g. pre- and post-aligner files) which can help with debugging poor alignments.

Default: False