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University of Bologna · MSc Bioinformatics · 2026

Molecular
Phylogenetics

16 lectures · Theory & practicals · Curated by Giobbe Forni

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Course Syllabus
CodeLectureMaterial
Week 1
W1_L01Intro to the course & software installationslides·practicals·docker setup·questions
W1_L02Phylogenetics 101 — Part Aslides·practicals·transcript·lab notes
W1_L03Phylogenetics 101 — Part Bslides·practicals·refresher·lab notes
Week 2
W2_L04Orthology inference and taxon samplingslides·practicals·lab notes
W2_L05Sequence alignment and filteringslides·practicals·lab notes
W2_L06Distance-based vs character-based algorithmsslides·practicals·lab notes
Week 3
W3_L07MK models of molecular evolutionslides·practicals
W3_L08Maximum Likelihood (ML)slides·practicals
W3_L09Bayesian Inference (BI)slides·practicals
Week 4
W4_L10Support metricsslides·practicals
Week 6
W6_L11Complex substitution modelsslides·practicals
W6_L12Discordance, ILS & the coalescentslides·practicals
Week 7
W7_L13Stochastic and systematic biasslides·practicals
W7_L14Divergence times analysesslides·practicals
Week 8
W8_L15Inferring selectionslides·practicals
W8_L16Modelling trait evolution on phylogeniesslides·practicals
Other Important Stuff
📋Available

Exam Sample

Representative exam questions and expected answer format.

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🎬Available

Lecture Recordings

Video recordings of all lectures. Available after each session.

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📦Coming soon

All Slides (Pack)

Download all lecture slides as a single archive.

Course Data

Course datasets including OrthoFinder results, example alignments, trees, and more.

git clone https://github.com/for-giobbe/MP26.git
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OrthoFinder results
data/OrthoFinder/
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Single copy orthologues
data/Single_Copy_Orthologue_Sequences/
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Example alignments
data/example_alignements/
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Example trees
data/example_trees/
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Example dating
data/example_dating/
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Example selection
data/example_selection/
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Proteomes
data/proteoms/
Instructors
GF

Giobbe Forni

Course Curator

giobbe.forni2@unibo.it
JM

Jacopo Martelossi

Contributor

AL

Andrea Luchetti

Contributor