geneid 1.4.4: New formula

geneid is a program to predict genes in anonymous genomic sequences
designed with a hierarchical structure.

http://genome.crg.es/software/geneid/
genewise 2.4.1: New formula

Wise2's key programs are genewise, a program for aligning proteins or
protein HMMs to DNA, and dynamite a rather cranky "macro language"
which automates the production of dynamic programming.

http://www.ebi.ac.uk/~birney/wise2/
cegma 2.4.010312: New formula

CEGMA (Core Eukaryotic Genes Mapping Approach) is for building a
highly reliable set of gene annotations in the absence of experimental
data.

http://korflab.ucdavis.edu/datasets/cegma/