Lin MF, Jungreis I, Kellis M.

Bioinformatics. 2011 Jul 1;27(13):i275-82. doi: 10.1093/bioinformatics/btr209

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.

Classifies coding and non-coding regions using multiple genome sequence alignments and the fit with separate codon score matrices for coding an non-coding.