Many components of phylogenetic inference belong to the most computationally challenging and complex domain of problems. To further escalate the challenge, the genomics revolution has exponentially increased the amount of data available for analysis. This, combined with the foundational nature of phylogenetic analysis, has prompted the development of novel methods for managing and analyzing phylogenomic data, as well as improving or intelligently utilizing current ones. In this study, a novel alignment tree building algorithm using Quasi-Hidden Markov Models (QHMMs), Scrawkov-Phy, is introduced. Additionally, exploratory work in the design and implementation of an extensible phyloinformatics tool, EMU-Phy, is described. Lastly, features of the best-practice tools are inspected and provisionally incorporated into Scrawkov-Phy to evaluate the algorithm’s suitability for said features.

This study shows that Scrawkov-Phy, as utilized through EMU-Phy, captures phylogenetic signal and reconstructs reasonable phylogenies without the need for multiple-sequence alignment or high-order statistical models. There are numerous additions to both Scrawkov-Phy and EMU-Phy which would improve their efficacy and the results of the provisional study shows that such additions are compatible.

Library of Congress Subject Headings

Cladistic analysis; Phylogeny; Algorithms

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Larry J. Buckley

Advisor/Committee Member

Michael V. Osier

Advisor/Committee Member

Gregory A. Babbitt


Physical copy available from RIT's Wallace Library at QH83 .F47 2016


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