BIO9905FBI2 - Phylogenomics

Course content

Phylogenomics is a group of techniques within the larger

fields of phylogenetics and genomics, and focuses on

genome data and evolutionary reconstructions.

Phylogenomics draws information by comparing entire

genomes, or at least large portions of genomes.

Learning outcome

Advances in high-throughput sequencing and genomics have

revolutionized research in evolutionary biology and

systematics. The use of genomics data in phylogenetic

analyses has brought new challenges in terms of data

handling and analysis. This course aims to help those that

have basic experience in bioinformatics and molecular

phylogenetics, and have projects focused on high-throughput

sequencing data and phylogenetics, to become acquainted

with tools, programs and pipelines for phylogenomics and

want to contact phylogenomic studies beyond the standard

also addressing potentially confunding biases in their datasets.

Admission

PhD candidates from the University of Oslo should apply for classes and register for examinations through Studentweb.

If a course has limited intake capacity, priority will be given to PhD candidates who follow an individual education plan where this particular course is included. Some national researchers’ schools may have specific rules for ranking applicants for courses with limited intake capacity.

PhD candidates who have been admitted to another higher education institution must apply for a position as a visiting student within a given deadline.

In addition to registering through Studentweb, all students are requested to apply by filling the course registration form that you find at http://www.forbio.uio.no/events/courses/2016/phylogenomics.html

Deadline August 1th.

The course is limited to 26 students. The course is arranged by the National research School in Biosystematics, ForBio. Priority will be given to members of ForBio.

Prerequisites

Recommended previous knowledge

BIO4200, BIO9905FBI1

Pre-course exercises on command line, regex and UNIX will be offered.

Teaching

The workshop will consist of lectures and hands-on work

aiming to provide the participants with a good working

knowledge of genomic data for phylogenomics, and to

become acquainted with tools, programs and pipelines for

phylogenomics. To encourage discussion, participants will

work in pairs most of the time. All exercises will be carried out

using example data handed out by the teachers during the

workshop, but all exercises and results can be readily transposed to individual research data.

Examination

The examination will consist of two written reports on provided case studies. The reports will need to be submitted within two weeks after each week of the workshop (report 1 for week 1, and report 2 for week 2). The reports must be approved to pass the course and receive a grade and credit.

Language of examination

The examination text is given in English, and you submit your response in English.

Grading scale

Grades are awarded on a pass/fail scale. Read more about the grading system.

Explanations and appeals

Withdrawal from an examination

It is possible to take the exam up to 3 times. If you withdraw from the exam after the deadline or during the exam, this will be counted as an examination attempt.

Special examination arrangements

Application form, deadline and requirements for special examination arrangements.

Facts about this course

Credits

5

Level

PhD

Teaching

Autumn 2016

One week in November and one week in April

Examination

Spring 2017

Teaching language

English