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.