Phylogenetic Cartography: Automating Genetic Database Searching and Spatial Analysis
From 15 Dec 2025 until 17 Dec 2025 - BIOPOLIS-CIBIO, Vairão, Portugal (Face-to-face)
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), automate data queries and species identification and integrate them with spatial biodiversity databases (e.g. IUCN, GBIF). Automatized procedures will be conducted mainly in R and occasionally in python; preliminary knowledge on the former environment is recommended.
PROGRAM
- Day 1 (morning) – Review on genetic data and databases: sequencing techniques, data types and formats, alignments, online repositories, applications. Review on phylogenetic tools: trees, networks, clustering. Introduction to high-throughput data and databases.
- Day 1 (afternoon) – Working with genetic data: i) chromatogram verification, sequence correction and alignments; ii) phylogenetic trees and haplotype networks. Working with High-throughput data.
- Day 2 (morning) – Working with genetic data: iii) taxonomic identification.
- Day 2 (afternoon) – Working with genetic data: iv) distance-based species’ delimitation methods (genetic matrixes, barcoding gap); v) coalescence-based species delimitation methods.
- Day 3 (morning) – Spatial biodiversity databases. Download, verification and visualization of spatial data. Integration of spatial and genetic data.
- Day 3 (afternoon) – Geostatistics. Genetic diversity interpolations. Phylogenetic mapping.
CALENDAR
3 days - 21 hours - Schedule: 09:30 - 13:00 & 14:00 - 17:30
COURSE INSTRUCTORS
Coordination
André Vicente Liz | CISPAC/USC, BIOPOLIS-CIBIO
Duarte Vasconcelos Gonçalves | CIIMAR, BIOPOLIS-CIBIO
Instructor
Costanza Piccoli | BIOPOLIS-CIBIO
Duarte Vasconcelos Gonçalves | CIIMAR, BIOPOLIS-CIBIO
Instructor
Costanza Piccoli | BIOPOLIS-CIBIO
SELECTION CRITERIA
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)
APPLICATION
Deadline: 31 October 2025
To apply fill the FORM
A copy of your submitted form will be sent to the email address you provided. This email is your confirmation that the application was successfully submitted.
A copy of your submitted form will be sent to the email address you provided. This email is your confirmation that the application was successfully submitted.
If you don't receive this email, your application was not successfully submitted.
We will email you the results within 10 working days after the application deadline.
REGISTRATION
65€ (students) | 100€ (other participants).
BIOPOLIS/ CIBIO members will have an additional discount of 20%.
Participation is free of charge for BIODIV Students (M BGE & PhD) & CIBIO's TwinLabs members.
(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).
MORE INFORMATION
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.
CONTACT
Education & Training Unit (Post graduation office)
+351 252 660 425