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-msaout option


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.

1sco
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