genometools/genometools — pull request #306 by satta (2014-05-15 15:58:31+00:00)
Title: Add some tools for assessing coding capacity of ORFs

This PR adds some (still dev) tools fo calculating some intrinsic measures of coding capacity on CDS features, e.g.:
- the TESTCODE statistic, cf. Fickett, Nucleic Acids Res. 10(17):5303-18, 1982.
- a measure based on codon usage profiles, cf. Staden and McLachlan, Nucleic Acids Res. 10(1): 141–156, 1982.

These are implemented as streams which score and filter CDS features based on these measures. Also included is a tool to generate all ORFs from input sequences as well as a tool for counting codon usage in a given annotation-sequence pair.