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bioinformatics stuffs. any feedback or contributions would be greatly appreciated i can move code to github/bitbucket to facilitate that if it helps:

NOTE: as of 2009/10/13 some modules which previously lived here have been moved to bitbucket

  • gfftools: these mostly require genometools to work, but allow merging and sorting of existing gff files and drawing (using matplotlib) of gff files onto chromosomes.
  • ihash : this is a project to encode an interval to a string suitable for indexing in a b-tree, has the same limitations as geohash (http://en.wikipedia.org/wiki/Geohash), on which it is based.
  • interval_tree : a pure python interval tree that's extremely simple. also a shedskin version. for real work, use the interval tree in bx-python instead.
  • seqfind : a cython BKTree and damerau-levenshtein distance for indexing words/sequences.
  • scripts/dagchainer : scripts for and modifications to B. Haas' dagchainer for finding syntenic pairs.
  • scripts/localdups : find local (tandem) duplications given a simple input format.
  • scripts/mask_genome : given a full-genome BLAST output and a fasta file, create a masked version of the fasta based on the number of BLAST hits at each basepair location.
  • gtpym : a module to add some features to the genometools python library.
  • and more ...
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