A primer to molecular phylogenetics 29 March – 1 ... - Yves Desdevises

Feb 8, 2019 - A primer to molecular phylogenetics. 29 March – 1 April 2019. Yves Desdevises. Sorbonne Université France. Observatoire Océanologique de ...
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A primer to molecular phylogenetics 29 March – 1 April 2019 Yves Desdevises Sorbonne Université France Observatoire Océanologique de Banyuls-sur-Mer

Planning

AM Course 9:00-12:00 Friday 29 March

Trees



Sequence retrieval from GenBank



Molecular data



Alignment



Alignment



Model selection



Evolutionary models



Parsimony



Maximum Likelihood (ML)



Tree Validation

Course 9:00-12:00 Sunday 31 March

Practical 14:00-18:00 •

Molecular phylogeny via parsimony, ML, and distance



Tree validation

Practical 14:00-18:00



Bayesian Inference (BI)



Molecular phylogeny via BI



Distance methods



Data combination



Data combination

Practical 9:00-12:00 Monday 1 April

Practical 14:00-18:00



Course 9:00-12:00 Saturday 30 March

PM

Course 13:30-15:30



Topology tests



Tree comparison



Supertrees



Supertrees



Case study



Phylogenomics

Software used: PAUP*, MEGA 7, MrBayes, PhyML, RaxML, jModelTest, ProtTest, MAFFT, GBlocks, FigTree, Clann

IQ-Tree,

8/02/19