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A collection of phylogenetics tutorials delivered to colleagues at the Centre for Biological Control (CBC). Topics include producing Bayesian and Maximum Likelihood trees, haplotype networks, reading phylogenies into R, analysing ISSR and SSR data, and using STRUCTURE and SplitsTree.

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CBC Tutorials with Clarke 📖

Welcome to the CBC tutorials repository!

This is where you can find a variety of helpful tips and tricks for phylogenetic analyses, and just general neat things to do in R. Please email me at [email protected] if you have any questions or suggestions, or if you have some useful tips that you would like to share!

📌 Each tutorial folder contains an instruction file with the extension .md

For phylogenetic tutorials, you need the following software:

BioEdit is also widely used, but I prefer AliView as it can be used on multiple operating systems https://bioedit.software.informer.com/7.2/

We'll go through using Inkscape later, for graphical editing https://inkscape.org/

Useful online servers:

CIPRES (for running various analyses on a server) http://www.phylo.org/

EMBOSS seqret (for converting between file types, e.g. FASTA <-> NEXUS) https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/

MAFFT (for multiple sequence alignment) https://mafft.cbrc.jp/alignment/software/

🎥 YouTube tutorials:

Make your own R package:

PART1: https://www.youtube.com/watch?v=pMq42QT8AbE&t=7s (Basic setup)

PART2: https://www.youtube.com/watch?v=1woJqeZCuog&t=34s (Adding a vignette)

PART3: https://www.youtube.com/watch?v=QsNAhukSw1g&t=59s (Embedding example data into the package)

A guide to the BinMat R package for fragment analysis data

PART1: https://www.youtube.com/watch?v=RTHf7Naqr10

PART 2: https://www.youtube.com/watch?v=jk4uBzVgqw8

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A collection of phylogenetics tutorials delivered to colleagues at the Centre for Biological Control (CBC). Topics include producing Bayesian and Maximum Likelihood trees, haplotype networks, reading phylogenies into R, analysing ISSR and SSR data, and using STRUCTURE and SplitsTree.

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