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Phylogenetics - Back to Basics - Introduction

Michael Charleston

Updated: PURL: gxy.io/GTN:S00116

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Requirements

Before diving into this slide deck, we recommend you to have a look at:

Introduction to Galaxy Analyses

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Hand drawn phylogenetic tree from Charles Darwin’s notebook with clades A, B, C, D branching from a common ancestor. Prefaced with handwriting that reads ‘I think’ and annotated with other illegible notes.

Charles Darwin, 1837 Notebeook entry

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Model of the external structure of the SARS-CoV-2 virion

https://en.wikipedia.org/wiki/Coronavirus; CC BY-SA 4.0

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Two-part figure showing a phylogenetic tree of SARS-CoV-2 strains on the left and genomic epidemiology of SARS-CoV-2 with subsampling focused globally over the 6 months leading up to November 2023 on the right https://nextstrain.org/ncov/gisaid/global/6m

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Covid-19, latest tree from NextStrain

Phylogenetic tree for SARS-CoV-2 strains coloured by strain grouping

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Terminology

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Phylogenetic tree of hexapods

Circular phylogenetic tree of hexapods (insects). Clades are colour coded and labelled with common names e.g. ‘Fleas’. Silhouettes of representative species are shown around the outside of the tree. https://doi.org/10.1371/journal.pone.0109085; CCBY 4.0 DEED license

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Sequence alignment

Screenshot of sequence visualisation output from Galaxy. Fifteen Anolis DNA sequences are arranged in rows. The nucleotides are colour coded and arranged in columns: A(blue), T (green), C (pink), G (orange). The top half of the image shows approximately 50 bases of each sequence. The lower half of the image shows a zoomed out heatmap-like image of a larger portion of the sequences.

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Building trees from distances

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Searching for trees

Screenshot of a phylogenetic tree of Anolis species. The root of the tree is on the left and the species are listed vertically on the right. The tree consists of multiple branching events and clades and includes bootstrap values.

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Phylogenetic Networks

Screenshot of a phylogenetic network of Anolis species. The root of the network is at the centre of the image and clades radiate outwards forming a circular network.

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Thank you!

Let's begin

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Thank You!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!

Author(s)	Michael Charleston
Reviewers

Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.

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Phylogenetics - Back to Basics - Introduction

Requirements

Covid-19, latest tree from NextStrain

Terminology

Phylogenetic tree of hexapods

Sequence alignment

Building trees from distances

Searching for trees

Phylogenetic Networks

Thank you!

Thank You!

Requirements

Help