circuclust

Circular alignment and clustering of nt sequences.

all-vs-all circular global alignment of query-vs-database:

  circuclust -align query.fa \
	-db db.fa \
	-output alignments.txt \
	-tsvout hits.tsv \

Cluster using UCLUST algorithm with circular global alignment, both plus and minus strands are checked, minimum fractional identity is specified by -id option:

  circuclust -cluster seqs.fa \
 	-id 0.9 \
	-fastaout centroids.fa \
	-tsvout hits.tsv

Download pre-compiled binaries

Go to Releases at the github project home https://github.com/rcedgar/circuclust/releases.

Compile from source

Linux: The gcc compiler and make are required. Clone / download the repository, go to the src/ sub-directory and type make. If successful, the binary will be in the bin/ sub-directory.

Windows / Visual Studio: Load and build the circuclust.sln solution file.

Mac and Windows Cygwin: The Linux Makefile should work more or less, not tested so some tweaking may be needed.