BIO9905FBI2 – Phylogenomics
Course description
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 to the course
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 contact the department of biosciences before April 10th at studieinfo@ibv.uio.no
In addition to registering through Studentweb, all students must apply for admission at the link at: https://www.forbio.uio.no/events/courses/2018/phylogenomics2018.html
Deadline April 15th.
The course is limited to 12 students. The course is arranged by the National research School in Biosystematics, ForBio. Priority will be given to members of ForBio.
Recommended previous knowledge
Pre-course exercises on command line, regex and UNIX will be offered.
Overlapping courses
- 5 credits overlap with BIOS9905FBI2 – Phylogenomics.
Teaching
The workshop will be given in fall 2021 and 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 consists of independent application of the learned methods to simulated datasets on the final course day. The results of this application must be presented and approved to pass the course and receive a grade and credit.
Exam attempts
It will be counted as one of the three attempts to sit the exam for this course, if you sit the exam for one of the following courses: BIOS9905FBI2 – Phylogenomics
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.
More about examinations at UiO
- Use of sources and citations
- Special exam arrangements due to individual needs
- Withdrawal from an exam
- Illness at exams / postponed exams
- Explanation of grades and appeals
- Resitting an exam
- Cheating/attempted cheating
You will find further guides and resources at the web page on examinations at UiO.