augur align

Align multiple sequences from FASTA.

usage: augur align [-h] --sequences SEQUENCES [--output OUTPUT]
                   [--nthreads NTHREADS] [--method {mafft}]
                   [--reference-name REFERENCE_NAME]
                   [--reference-sequence REFERENCE_SEQUENCE]
                   [--remove-reference] [--fill-gaps]

Named Arguments

--sequences, -s

sequences in fasta or VCF format

--output, -o

output file

--nthreads

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

--method

Possible choices: mafft

alignment program to use

Default: “mafft”

--reference-name

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

--reference-sequence

strip insertions relative to reference sequence; use if the reference is NOT already in the input sequences

--remove-reference

remove reference sequence from the alignment

Default: False

--fill-gaps

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

Default: False