PhD in Biological Sciences and Applied Biotechnologies

Workshop on R software in phylogenetic analyses

Sommario del corso

• Course objectives
• Results of learning outcomes
• Program
• Teaching tools
• Course card

Course objectives

Workshop on R software in phylogenetic analyses

This workshop will consist of an introduction to basic concepts of phylogenetic and comparative methods (especially the ones available for studies of macroevolution), and the tools available in R language for evolutionary analyses. 

The workshop will be on

November 28 (9.00 - 13.00) and

November 29 (9.00 - 13.00; 14.00 - 17.00)

at DBIOS, V. Accademia Albertina 13, Torino

Aula 4

Lessons will be in English

Course instructors:

Francesco Santini (visiting fellow, Universita' di Torino)
Laurie Sorenson (University of California Los Angeles)

Registration to the workshop is requested and can be done by sending an email message to the local organizer:

sergio.castellano@unito.it

.

Results of learning outcomes

Students will learn how to enter and manipulate data matrices and trees in R, reconstruct ancestral states on a phylogeny, and identify patterns and estimate rates of lineage and character evolution through time.

Program

(i) Introduzione a R, installazione di R e pacchetti, aggiornamento
pacchetti, vettori, costruzione di dataframe e matrici, creare dati,
input e output di dati

(ii) importare matrici di dati da file nexus, phylip, fasta, csv,
excell, conversione di tipi di file, lavorare con alberi
filogenetici, leggere e scrivere alberi in vari formati (ese. newik,
nexus), manipolazioni grafiche, come creare figure publicabili.

(iii) modelli di evoluzione dei caratteri (OUCH, AUTEUR), testare
ipotesi di selezione naturale.

(iv) introduzione allo studio della diversificazione, gamma e test
MCCR, lineages through time (ltt) plots, disparity through time
(dtt) plots, medusa; diversitree (bisse, musse) per alberi completi
e incompleti, test di innovazioni chiavi.

(v) ricostruzione stati ancestrali (maximum likelihood, modello
mk1).

• Teaching material
• Exams and finals
• Class schedule
• Go to Moodle
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