New release with minor bug fixes

Added code to append the Cuffcompare sample name (without "combined.gtf") to the outputs of the Evolinc so that it will be easy for downstream analysis.

Minor bug fixes

We fixed a couple of minor bugs namely:

• Fixed the typo (from AGE_PLUS to CAGE_PLUS)
• Add the requisite library (library(data.table))
• Updated the README accordingly

Final TE update

v1.7.3

Last TE fix

All TE steps fixed

v1.7.2

Fix lastdb TE input

rFAM fix

Fixed some file name issues with the rFAM step.

rFAM filter added

We added an rFAM filter step and replaced BLAST algorithm with LAST.

Much faster Evolinc-I release

As part of this new release, the following were installed

• Diamond blastp which is 20,000 faster than the regular fast
• Added a script to resolve overlapping transcripts

Evolinc -I with CPC2 with additional flag

• Performed some more bug fixes and clean up jobs.
• Added an additional flag for cpc2 to look for reverse strand as well
• Modified REAMDE.md

Evolinc -I with CPC2 release

CPC2 code added:

Added code to filter class codes transcript, to filter gffcompare gff output and finally CPC2-beta software was added to filter out coding transcripts before transdecoder

Manuscript published

Manuscript published in Frontiers in Genetics.

• Update README with the new version of Docker image
• Add citation for Evolinc
• Ready for public release