The malaria parasite Plasmodium falciparum, is a eukaryotic protozoan that infects a third of the global population and causes more than 2 million deaths per year. With new genome information available for this parasite, there is an increasing need for computational analysis on this relatively unstudied genome. This research project seeks to create a set of gene predictions for the P. falciparum genome which are more accurate than the predictions currently available for this protozoan. Our methods include using the genome wide multiple alignments compiled between several species of malarial parasites to run a phylo-HMM which predicts conserved coding regions in the genome. The method of gene prediction in this project is to retrain the ab initio HMM gene finder for P. falciparum. Better ab initio gene predictions will provide researchers with a better foundation to identify possible drug targets to fight this deadly disease.