The -msaout option of the cluster_fast and
cluster_smallmem commands specifies a
FASTA file to contain a multiple alignment for
each cluster. The multiple alignment is produced by a very fast method that is
designed for high identity thresholds. At lower identities, the alignment will
tend to have lower accuracy than specialized methods such as
MUSCLE. Supported in v6.0.307 and later.
Note that -msaout must store
alignments of all members of a cluster until the clustering command completes.
This may require substantially more memory than clustering without -msaout.