Aligned sequences are produced as a result of the sequence alignment step and are being output in FASTA format.
All alignments are with respect to the reference sequences.
Nextclade Web: download
Nextclade CLI argument:
<FILENAME>. If the CLI flag
--include-reference is set, the reference sequence is included as the first entry.
⚠️ Note that if alignment or analysis of an individual sequence fails, it is omitted from the output alignment file. See Errors and warnings section for more details.