gene calling tools

[RNAer]

This was brought up during the discussion with @idoerg and @mortonjt . The most competent tools seem including 1) GeneMark, 2) Glimmer, and 3) Prodigal. The first option we choose here, prodigal, is based on literature. A paper shows Prodigal performs better, according to their benchmark:

1. Pati,A., Ivanova,N.N., Mikhailova,N., Ovchinnikova,G., Hooper,S.D., Lykidis,A. and Kyrpides,N.C. (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Meth, 7, 455–457.

This is open for discussion and plugin other tools if they are better for gene calling.