Major updates, speed improvements, and minor bug fixes

Replaced BLAST with Minimap2 (100x speed improvement).
Upgraded the Dockerfile to Ubuntu 18 and Python3, etc (the 21st century).
Evolinc-II now checks FASTA headers and removes some of the more annoying features that cause failures (spaces, underscores, etc).
The batch analysis steps for the phylogenetics, gene duplication/loss, and RNA structure now pull in the thread/CPU information provided at the beginning (another speed improvement).
Added a new plot (UpSet Plot) that better describes where lncRNA homologs are identified and in what combination of species.
Added color to the bar plot used to depict overall recovered homologs per species.
Added a RNA structural analysis step that utilizes multiple sequence alignments (more powerful form of structure inference). This drags on speed however, so should not be performed on large data sets without many threads.

A host of other minor bugs that occur under special circumstances.

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

Manuscript (Preprint) submission (bug fix release)

Bug fix release

• Added a line in Building_Families.sh to address an input file with a single lincRNA

Manuscript (Preprint) submission

The Evolinc-II v1.0 is thoroughly tested using Docker image on Linux and as Evolinc-II v1.0 app on CyVerse Discovery Environment. The compressed sample data is attached to this release