clustertools

This is a bunch of stuff I needed at some for manipulating sequence clusters. See the README for details. The tools included are: filter - remove unwanted sequences from a clustering hist - produce a histogram of cluster sizes from a "label"-formatted clustering. clusc - compare clusterings, calculating numerous pair-based and entropy based indices. add_single - add singletons to a clustering. ace2contigs - parse an ACE assembly file, and output the contigs in a FASTA file. ace2fasta - parse an ACE assembly, and output each assembly in a separate FASTA file ace2clusters - parse an ACE assembly, and output clusters in TGICL format clusterlibs - given a table of regular expressions and library names, along with a clustering (TGICL-format), output a table of cluster sizes per library. xcerpt - extract sequences from a list of sequence labels. The Darcs repository is at: http://malde.org/~ketil/biohaskell/cluster_tools.