Phylogenetic Cartography: Automating Genetic Database Searching and Spatial Analysis
Event
April 26th, 2027
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
COURSE INSTRUCTORS
Coordination
André Vicente Liz | CISPAC/USC, 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
Official applications for this course will be managed directly by FCUP. Detailed information will be available soon.
If you would like to be notified as soon as registrations open, please let us know by filling out our short form: Express Your Interest Here
⚠️ Please note: This form is not an official application. It simply allows us to keep you updated and helps us gauge the level of interest for each course.
MORE INFORMATION
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