A wonderful description of phylogenetics can be found on wikipedia here. But to put it in our own terms - Phylogenetics is the study of the relationships between species. Such as how chimps and homo sapiens share many common ancestors though nearly none in common with the noble radish. The reconstruction refers to taking present day information and using it to infer on what the past structure of the tree of life may have looked like. In our case we looked exclusively at DNA sequences.
We chose to complete a survey paper on the field of Phylogenetic Reconstruction in an effort to feel out the best tools to go from DNA to fully fledged Phlyo trees. In the paper you will find the sum of our knowledge as well as the results from our own experiments using the alogrithms we learned from previous researchers. In the code you will find all of our implementations of the algorithms used.
THE PAPER
Our project culminated in a paper we wrote to convey all that we've learned about the field of Phylogenetic Reconstruction. You are encouraged to take a look, but we remind you it is currently unpublished.
THE CODE
Our project's coding can be found in a zip file from the link below. The code is written primarily in C++ and relies only on boost libraries and cmake to compile. Though some scripts used are written in java and python.
EVAN ALBRIGHT
The thunder-god, Evan, spent his formative years wrestling chimera in the pits of tartarus so that he may one day prove to his father Zeus he would be worthy of the Olympic Throne. Born without a sense of humor, Evan is prone to fits of hysteria when within three city blocks of a birthday clown. Evan once forgot who he was for three years when his friend double-dog dared him to. During the duller hours of life Evan finds himself coding and striving for self-betterment in all things, secretly dreaming of the day he can unleash skynet on the world.
JACK HESSEL
Born in far warmer lands, Jack's newly frozen demeanor keeps his CPUs well within acceptable temperature ranges. Stuck somewhere between theorist and engineer, he continues his never ending struggle to find problems that make him annoyed enough to solve them. He can often be found hunched over his keyboard, unconsciously dancing to electronic music his grandmother can only describe as "noisy." When not operating a data processor, Jack enjoys playing ice hockey, eating vegetables, and taking long, romantic walks on the beach.
NAOZUMI HIRANUMA
Nao Hiranuma is best known as the strongest samurai warrior in the present day. The excellence in his swordsmanship was known since he was 2 years old. He has won over 200 duels so far and still undefeated. Aside from being a great sword-master, he is interested computer science, especially evolutionary computing and machine learning. Starting next year, he will continue his education in the universal Jedi academy in order to enrich his energy sword techniques.
YUANBO (CODY) WANG
As a Poker master, Cody seldom bluffs when he faces the majesty of computers and big data. Since 4 years ago when he joined the table, he has remained the chip leader despite those ups and downs, with a particular deep stack of Lay's Barbecue chips. A member of the Phylo team, he has always strived to be the best in their quest of searching for primates far and wide, and is on the way to completing his beloved Pokédex.
Sherri Goings - Advisor