This is a fix release to address several issues reported by our users:

• Several Cuffmerge bugs have been fixed. One of these caused Cuffmerge to fail with a message about chromosome sort ordering.
• A comment parsing issue in Cuffmerge has been fixed.
• GTF files emitted by Cuffcompare are now lexicographically sorted by chromosome.
• Gffread now has some transcript clustering and redundancy reduction features, similar to those found in Cuffcompare
• The header size limit in Cufflinks’ BAM parser used to have a 4 megabyte limit. This has been removed to allow Cufflinks to be used on assemblies with many contigs.