W1_L01
Intro to the course & software installation
MP26 · Molecular Phylogenetics
A complete, ready-to-run Docker environment for the MP26 Molecular Phylogenetics course. Everything is pre-installed — R packages, bioinformatics CLI tools, and the full course repository. No setup, no compilation, no dependency issues. Pull the image and start working in under a minute.
Requirements
- Docker (any platform — Linux, macOS, Windows)
Quick start
docker run -d -p 80:80 -p 8787:8787 -p 8080:8080 \
-e PASSWORD=phylo123 --name mp26 \
mahmoudxyz/mp26-phylo
Open http://localhost in your browser. That's it.
What's inside
Course data
The full MP26 GitHub repository is pre-cloned at ~/MP26, including all example alignments, trees, sequences, and practical data.
Browser tools
| URL | Tool | Purpose | Login |
|---|---|---|---|
| http://localhost | Hub | Overview, instructions, git pull | — |
| http://localhost:8787 | RStudio | R practicals | rstudio / phylo123 |
| http://localhost:8080 | File browser | Browse, upload, download files | — |
R packages
| Package | Source |
|---|---|
| Biostrings | Bioconductor |
| msa | Bioconductor |
| apex | Bioconductor |
| ape | CRAN |
| seqinr | CRAN |
| phangorn | CRAN |
| phytools | CRAN |
| geiger | CRAN |
CLI tools
| Tool | Purpose |
|---|---|
| mafft | Multiple sequence alignment |
| gblocks | Alignment filtering |
| iqtree / iqtree2 | Maximum likelihood phylogenetics |
| paml / codeml | Selection analysis (dN/dS) |
| astral | Coalescent-based species tree |
| orthofinder | Orthology inference |
| phylobayes / pb_mpi | Bayesian phylogenetic inference |
| prank | Codon-aware alignment |
| amas | Alignment concatenation |
| ete3 | Python tree toolkit |
Pretty output tools
| Tool | Use |
|---|---|
bat | Syntax-highlighted file viewer (cat replacement) |
eza | Modern directory listing (ls replacement) |
mlr | TSV/CSV/JSON swiss army knife |
csvkit | csvlook, csvstat, csvcut for tabular data |
Terminal access
Open your system terminal and run:
docker exec -it mp26 bash
You land directly in ~/MP26 with all tools on PATH and these aliases ready:
tsv file.tsv # pretty-print any TSV file
csv file.csv # pretty-print any CSV file
bat file.txt # syntax-highlighted file view
ll # detailed directory listing
Mount your own files
To bring local files into the container:
docker run -d -p 80:80 -p 8787:8787 -p 8080:8080 \
-e PASSWORD=phylo123 --name mp26 \
-v ~/mydata:/home/rstudio/mydata \
mahmoudxyz/mp26-phylo
Your files appear at ~/mydata inside RStudio, the terminal, and the file browser.
Update course materials
From the hub, click git pull. Or from the terminal:
docker exec mp26 update_repo.sh
Stop / restart
docker stop mp26 # stop the container
docker start mp26 # restart it (all data preserved)
docker rm -f mp26 # remove it completely
Change the password
Pass a different value to -e PASSWORD:
docker run ... -e PASSWORD=mypassword ... mahmoudxyz/mp26-phylo
Rebuilding from source
git clone https://github.com/mahmoudxyz/mp26-phylo-docker
cd mp26-phylo-docker
docker build -t mahmoudxyz/mp26-phylo .
Course
MP26 — Molecular Phylogenetics Course material by Giobbe Forni et al. · Docker image by mahmoudxyz