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This training school will guide you from how to make, use and modify and align fasta files, make maximum-likelihood time-scaled phylogenies, up to performing phylodynamic and phylogeographic analyses with BEAST. Everything can be followed remotely thanks to short GIFs and step-by-step guides.

If you use the methods described in this repository Wiki, please cite the following:

Richard, G., Byrne, A. M. P., Cavicchio, L., Chiapponi, C., Prosperi, A., & Fusaro, A. (2024, November 28). ESFLU WG2 Training School: Phylogenetics and Phylodynamics from Zero to Hero. Zenodo. https://doi.org/10.5281/zenodo.14234798

Gautier Richard ¹, Alexander M. P. Byrne ², Lara Cavicchio ³, Alice Fusaro ³.

1: ANSES Ploufragan‑Plouzané‑Niort Laboratory (ANSES-PPN), Swine Virology Immunology Unit, Ploufragan, France.

2: Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom.

3: Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viral Genomics and Transcriptomics, Padova, Italy.

Chiara Chiapponi ⁴, Alice Prosperi ⁴

4: Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Brescia, Italy.

ESFLU COST Action (CA21132):

• https://www.cost.eu/actions/CA21132/
• https://swineflu.eu/

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Make sure you install the following tools and that they are working on the computer you will bring to the training school:

• Windows:

  • AliView (sequence alignment viewer and editor): https://ormbunkar.se/aliview/downloads/windows/windows-version-1.28/without_installer_version/
  • Figtree(phylogenetic trees viewer and editor): https://github.com/rambaut/figtree/releases/download/v1.4.4/FigTree.v1.4.4.zip
  • Beast: https://beast.community/install_on_windows
  • TempEst: http://tree.bio.ed.ac.uk/download.html?name=tempest&id=102&num=2
  • Tracer: https://github.com/beast-dev/tracer/releases/download/v1.7.2/Tracer.v1.7.2.zip
  • BEAGLE: https://github.com/beagle-dev/beagle-lib/wiki/WindowsInstallInstructions

• Mac:

  • AliView (sequence alignment viewer and editor): https://ormbunkar.se/aliview/downloads/mac/AliView-1.28-app.zip
  • Figtree(phylogenetic trees viewer and editor): https://github.com/rambaut/figtree/releases/download/v1.4.4/FigTree.v1.4.4.dmg
  • Beast: https://beast.community/install_on_mac
  • TempEst: http://tree.bio.ed.ac.uk/download.html?name=tempest&id=102&num=1
  • Tracer: https://github.com/beast-dev/tracer/releases/download/v1.7.2/Tracer.v1.7.2.dmg
  • BEAGLE: https://github.com/beagle-dev/beagle-lib/wiki/MacInstallInstructions

• Linux:

  • AliView (sequence alignment viewer and editor): https://ormbunkar.se/aliview/downloads/linux/linux-version-1.28/
  • Figtree(phylogenetic trees viewer and editor): https://github.com/rambaut/figtree/releases/download/v1.4.4/FigTree_v1.4.4.tgz
  • Beast: https://beast.community/install_on_unix
  • TempEst: http://tree.bio.ed.ac.uk/download.html?name=tempest&id=102&num=3
  • Tracer: https://github.com/beast-dev/tracer/releases/download/v1.7.2/Tracer_v1.7.2.tgz
  • BEAGLE: https://github.com/beagle-dev/beagle-lib/wiki/LinuxInstallInstructions

Day 1 - Wednesday 16/10/2024

• 9h00 - 13h00:

  • Welcome everyone! Short roundtable to know each other a bit better.
  • Phylogenetics principles, theoretical part
  • Training school dataset presentation.
  • Fasta files manipulation and cleaing using AliView.

• 14h00 - 18h00:

  • Sequence alignment using MAFFT webserver.
  • Phylogenetic tree computation using IQTree webserver.
  • Phylogenetic tree visualisation using FigTree.
  • Advantages of ultra fast bootstraps compared to neighbour joining trees.

Day 2 - Thursday 17/10/2024

• 9h00 - 13h00:

  • Verifying the temporal signal of your dataset using TempEst.
  • Time-scaled phylogenetic tree computation using TreeTime webserver.

• 14h00 - 18h00:

  • Phylodynamics: theoretical presentation and examples.
  • Model selection XMLs creation using BEAUTi.
  • Phylogenetic tree computation with Beast (mock).
  • Determination of the most appropriate Model using Tracer: a tale of caterpillar, wiggles and MLE.

• Convivial evening in Brescia.

Day 3 - Friday 18/10/2024

• 9h00 - 13h00:

  • MCC Tree generation using TreeAnnotator.
  • Visualisation of the final tree in FigTree.
  • Phylodynamic analyses with BEAST: GMRF Skyride viral population reconstruction and Markov Jumps/Rewards

• 14h00 - 16h00:

  • Phylodynamic analyses with BEAST: Bayes Factors
  • BEAST and Evolaps: phylogeographic analyses
  • Closing remarks and open discussions about the training.