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cluster_agg command

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The cluster_agg command performs agglomerative clustering of sequences in a FASTA or FASTQ file.

Cluster linkage is specified using the ‑linkage option, which may be set to max (the default), min or avg.

Output is reported as a tree in Newick format specified by the -treeout option and/or as a clusters file specified by the -clusterout option. If a clusters file is specified, then the -id option must be given to specify the identity threshold.

The first step in the algorithm is to compute a distance matrix, which can be saved to a file by specifying the -distmxout option. See calc_distmx for options related to the distance matrix calculation and output file.


usearch -cluster_agg seqs.fasta -treeout tree.phy -clusterout clusters.txt -id 0.80 -linkage min