Page Index - gtrichard/esflu_wg2_phylodynamics GitHub Wiki

27 page(s) in this GitHub Wiki:

• Home
• ESFLU WG2 Training School: Phylogenetics and Phylodynamics from Zero to Hero
• Citation
• Authors
• Local Organizers
• Funding
• Prior to the start of the Training School:
• Program
• 0) Principles of virus phylogenetics-Principles-of-virus-phylogenetics)
• 1) Training data set presentation-Training-data-set-presentation)
• A) FASTA file manipulation and cleaning-FASTA-file-manipulation-and-cleaning)
• B) FASTA file alignment with MAFFT-FASTA-file-alignment-with-MAFFT)
• C) Maximum‐likelihood phylogeny with IQ‐TREE-Maximum%E2%80%90likelihood-phylogeny-with-IQ%E2%80%90TREE)
• D) Phylogenies visualization using FigTree-Phylogenies-visualization-using-FigTree)
• E) NJ vs ML phylogeny reconstruction-NJ-vs-ML-phylogeny-reconstruction)
• F) Temporal signal verification using TempEst-Temporal-signal-verification-using-TempEst)
• G) Phylogeny across time using TreeTime-Phylogeny-across-time-using-TreeTime)
• H) Phylodynamics: theory-Phylodynamics:-theory)
• I) Model selection XMLs creation using BEAUTi-Model-selection-XMLs-creation-using-BEAUTi)
• J) Phylogenetic tree computation with BEAST (mock)-Phylogenetic-tree-computation-with-BEAST-(mock))
• K) Determination of the most appropriate Model using Tracer: a tale of caterpillar, wiggles and MLE.-Determination-of-the-most-appropriate-Model-using-Tracer:-a-tale-of-caterpillar,-wiggles-and-MLE.)
• L) Combining Analysis Outputs and Computation of the Maximum Clade Credibility Tree-Combining-Analysis-Outputs-and-Computation-of-the-Maximum-Clade-Credibility-Tree)
• M) Timescale BEAST MCC tree visualisation with FigTree-Timescale-BEAST-MCC-tree-visualisation-with-FigTree)
• N) BEAST Phylodynamic analyses-BEAST-Phylodynamic-analyses)
• O) BEAST & EvoLaps Phylogeographic Analysis-BEAST-&-EvoLaps-Phylogeographic-Analysis)
• Z) Nextstrain-Nextstrain)
• ZZ) Downsampling datasets-Downsampling-datasets)