Phylogenetic Cartography: Automating Genetic Database Searching and Spatial Analysis

This course is intended to provide students with theoretical background and practical experience on the spatial analysis of genetic data, with a main focus on the bioinformatic tools available to automatise the search, preparation, analysis, and representation of single marker data. Students will learn how to clean and curate data, access and handle DNA data from online repositories (e.g. GenBank, BOLD), automate data queries and species identification and integrate them with spatial biodiversity databases (e.g. IUCN, GBIF). Automatised procedures will be conducted mainly in R and occasionally in python; preliminary knowledge on the former environment is recommended. 

- Day 1 (morning/theoretical) - Review on phylogenetic tools; applications and limitations of DNA barcoding and metabarcoding; and introduction to bioinformatic tools and online repositories.

- Day 1 (afternoon/practical) – From raw data to genetic databanks: cleaning, curation, and preparation of DNA data.

- Day 2 (practical) – Species genetic identification: BLAST analyses, DNA sequence mining, and phylogenetic tree production.

- Day 3 (practical) – Merging genetic and spatial data: geographic bank mining; and mapping.

3 days - 21 hours - Schedule: 09:30 - 13:00 & 14:00 - 17:30

Coordination

Andre Vicente Liz | BIOPOLIS/ CIBIO-InBIO

Duarte Vasconcelos Gonçalves | BIOPOLIS/ CIBIO-InBIO/ CIIMAR 

Instructor

Costanza Piccoli | BIOPOLIS/ CIBIO-InBIO

The course will be open to a maximum number of 20 participants. 

75% of available student slots are reserved for BIODIV students.

 Priority will be given to:

• 1st year and other PhD students attending the BIODIV Doctoral Program;

• PhD students attending other courses;

• Other post-graduate students and researchers.

(A minimum number of participants is required for the course to take place)

Deadline:  11 October 2024

To apply fill the FORM

A copy of the form will be sent to the email address you provide as proof that you have successfully submitted your application. Results will be emailed to you within 8 working days of the application deadline.

65€ (students) | 100€ (other participants).

BIOPOLIS/ CIBIO members will have an additional discount of 20%. Participation is free of charge for BIODIV Students MBGE 1st year Students & CIBIO's TwinLabs 

(If applicable, payment will be made to Associação BIOPOLIS - VAT No. 516033727. Information on the payment amount and the payment deadline will be sent together with the results notification, and a proforma invoice may be issued in due time).

Registration fees do not include accommodation or meals. 

No ECTS credits are awarded for attending the course. Participants receive a certificate of attendance without quantitative evaluation.