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Algorithms for Constructing the Tree of Life

The “Tree of Life” represents the inter-relationship amongst all living things on this Planet. The aim of this research is to investigate algorithmic approaches to the construction of the Tree of life.

Department: Computer Science, Systems Engineering

Supervised by: Dr. M. Manjunathaiah

The Placement Project

“It is a truly wonderful fact --- the wonder of which we are apt to overlook from familiarity --- that all animals and all plants throughout all time and space should be related to each other in groups”, said Charles Darwin in 1859 (in his book “Origin of Species”). This idea of inter-relationship was so crucial to Darwin that the only illustration that appeared in his book was a diagram of a family tree of species! The tree sought to explain new concepts of evolution of species --- how natural selection works over generations to induce structural variations and how these accumulate over time to produce speciation. Phylogeny refers to the history of a clustered pattern of bio-diversity --- a species and its relation with other species in time, modelled as a tree known as evolutionary tree. At the largest scale the whole group addressed in this historical account is the entire life on this planet --- know in the most celebrated form as the “Tree of Life”. Computational Phylogenetics is the algorithmic approach to the construction of evolutionary trees. This is driven by recent advances in genetics. Distance matrix based algorithms are defined using genetic distance as the measure of relatedness. There are a variety of other algorithmic approaches to the tree construction problem such as Branch and Bound, Dynamic Programming and Stochastic algorithms. Each approach uses a different “homology” – a measure of similarity, thereby producing different tree structures. The aim of this research is to make a comparative study of state-of-the-art algorithms in Computational Phylogenetics and draw conclusions on their relative merits. The proposed research study will be carried out under the supervision of the principal investigator.

Tasks

As part of the research study, a student will be expected to: • Perform literature survey • Study a class of algorithmic approaches • Install and evaluate existing software packages related to the approaches • Produce a technical report related to the findings from the research study

Skills, knowledge and experience required

It is essential that the student should : • Have strong background in algorithmic techniques • Be proficient in programming • Have good technical report writing skills • Have strong motivation for research work

Skills which will be developed during the placement

• Experience in research methods of making comparative studies. • Knowledge of algorithmic approaches in tackling Biological problems. • Introduction to stochastic and randomized algorithmic approaches which can benefit a student in producing a high quality part 3 project. • Technical report writing skills and a potential publication that can enhance a student’s CV.

Place of Work

UoR

Hours of Work

Approximate Start and End Dates (not fixed)

Unknown - Unknown

How to Apply

Applications in the form of a CV from suitable candidates with a covering letter stating why the student feels he/she is qualified for the research placement may be submitted to m.manjunathaiah@reading.ac.uk


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