#1: JustOrthoGroups
-Revised JustOrthologs for use on any protein sequence
-Analyze the lengths of all CDS regions in different taxonomic groups
-Determine percent overlapping k-mers in each gene
-Apply "pseudo CDS" filter on genes sorted by length
-Compare k-mer composition {k-mer: count}
#2: ALS Drug Target
-DCA of PASK and ATXN2
#3: Direct Coupling Analysis of All Orthologs
-Make DCA faster and more memory efficient
-Run JustOrthologs on all vertebrates
-Run DCA on all pairwise comparisons of orthologs
#4: JustTrees: Highly Adaptive Phylogeny Visualization
-Hiring a computer science major to develop the software
Features:
1. Fully editable so that users can correct misspelled taxa on the tree
2. Easily color specific clades with one or more colors, including an optional legend
3. Able to add arrows (to point to regions) or other clip art to any part of the phylogeny
4. Easily add clade pictures from http://phylopic.org/
5. Variable and editable font sizes/ font type/ branch lengths
6. Collapsible clades so that large trees can be condensed
7. Support horizontal gene transfer with dashed lines
8. 3D drag (for web/app) for viewing horizontal gene transfer relationships better
9. Be able to copy the phylogeny without saving it
10. Save phylogeny as a JPEG, PNG, and SVG
11. Auto-format the smallest clades to the top of the phylogeny
12. Support JSON format for reading and exporting. Also support legacy formats
13. Option to manually add/remove taxa
14. Option to align taxa to the far right
15. Option to make all edges equal sizes
16. Option to make edges square or rounded
17. Add bootstrap/ custom labels
18. Format phylogeny to fit on a single page.
a. Support tall and skinny phylogenies
b. Support short and fat phylogenies
19. Option for circular phylogeny
20. Option for phylogeny/ clade titles
21. Option for a watermark