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.