I have been a part of a few programs in Masters and Ph.D. at SDSU and UCR. I outline some of them below. The rest are on github: ​https://github.com/aortizsax

Autophy

Autophy is a post-phylogenetic analysis of protein families to uncover novel subfamily functionality and fix mis-annotations through partitioning their phylogenetic tree.  The pipeline for stable phylogenetic partitioning uses maximum likelihood and is unsupervised, meaning that it targets to partition family with out a preconceived notion of its function and therefore aids in identifying mis-annotations.  

Zero-Curv

Zero-Curv is a program used to identify which features to keep in a count table.  Current study's arbitrarily remove feature that are present in 10-40% of the data, arbitrarily .  Zero-Curv aims to define a recommended cutoff using log transformations and curvature.  Interestingly, it is also functional when deciding a minor allele frequency cutoff. 

Future projects:

• Allelic information flow 
• A lil something secret for cancer ;)