Cuffmerge is part of Cufflinks.
Cuffmerge takes Cufflinks’ GTF output as input, and optionally can take a “reference” annotation (such as from Ensembl).
Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms.
C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, L. Pachter.
Nature Biotechnology (2010) 28, 511-515