Looking for novel lncRNAs using PhyloCSF

Question

[g.quaiferyan]

Hey

The majority of lncRNAs aren't properly annotated so I recently generated a GTF file from my RNA-seq dataset using cufflinks. Now I want to go through the GTF and only pull out any sequences which aren't annotated lncRNAs and which have a "lncRNA-like" signatures using PhyloCSF. Does anyone know how to do this?

thanks