Welcome to the hands-on ETE Toolkit Phylogenomics practical course!
This document and the attached repository are intended to provide a practical guided tour covering most important features in the ETE Toolkit. For this, we use a fake biological dataset, so all examples and exercises are motivated by biological questions. You can see this course as a support material to the already available technical ETE documentation:
The course is divided into several sections organized by notebooks under the nb/ folder. Each section represents a common phylogenomic question and covers different aspects of the ETE toolkit.
All necessary data to run the exercise is in data.tar.gz. You should decompress the file in the root directory of this repository.
IMPORTANT: Note that data used in this course is manually manipulated to ensure the expected results Do not use it for real work!
To start practicing you just need to:
- [Setup the environment](Environment setup)
After many years of work, your lab has just isolated and sequenced a very interesting strain of the Aquifex aeolicus bacterium. This strain possesses a remarkable resistance to sulfur-rich environment.
To investigate it further, you decide to address an in depth phylogenomic study where your strain is analyzed in the context of other known sulfur-related organisms and reference species.
TaxID Sci.Name
224324999 Aquifex aeolicus (your new strain. TAXID does not exist)
224324 Aquifex aeolicus VF5
263820 Picrophilus torridus DSM 9790
273063 Sulfurisphaera tokodaii str. 7
525897 Desulfomicrobium baculatum DSM 4028
555778 Halothiobacillus neapolitanus c2
637389 Acidithiobacillus caldus ATCC 51756
673860 Aciduliprofundum sp. MAR08-339
713587 Thioalkalivibrio thiocyanoxidans ARh 4
743299 Acidithiobacillus ferrivorans SS3
933801 Acidianus hospitalis W1
1051632 Sulfobacillus acidophilus TPY
1121405 Desulfococcus multivorans DSM 2059
1158165 Thioalkalivibrio sp. ALMg11
1255043 Thioalkalivibrio nitratireducens DSM 14787
Start a blank notebook and try to work on the tasks proposed in the following notebooks:
| Topic | Tasks | ETE features |
|---|---|---|
| Preparing Genomic data | General advides | None |
| Building gene families | clustering homologous sequences | Tree basics, ete-build, ete-view |
| Building gene phylogenies | building and handling phylogenetic gene tree | Tree basics, ete-build, ete-view |
| Building Concatenated species trees | building contatenated species trees | ete-build supermatrix, PhyloTree collections |
| Comparing trees | Comparing tree topologies | ete-compare, Tree.compare |
| Linking trees to alignments | binding MSAs and PhyloTrees | SeqGroup, PhyloTree |
| Testing selection | Testing evolutionary hypothesis | ete-evol, codeml, visualization |
| Predicting evolutionary events | Duplication and Speciation event detection | Rooting, Standardizing, evol events |
| Linking to NCBI taxonomy | Querying NCBI taxonomy | ete-ncbiquery, NCBITaxa, Tree.annotate_ncbi_taxa |
| Annotation trees | NA | NA |
| Programmatic visualization | Custom visualization | tree.render, TreeStyle, NodeStyle, Faces |
this tutorial requires the following:
-
git (to clone and update this repository)
-
Python 3.6 (for full compatibility, avoid 3.7 and 3.8)
-
ete3 3.1.2 (Install lastest from etetookit conda channel, other channels might not be updated.
-
ete_toolchain (install from etetoolkit conda channel)
-
jupyter notebook and nbextensions
-
The recipe to obtain a clean environment to follow all steps bellow:
# makes a separate dir for this course and enter it
mkdir etecourse/
cd etecourse/
# clone this repository
git clone https://github.com/etetoolkit/course
- You can skip this step if you already have a conda env and know how to use it
- Rembember to initialize your conda env. i.e. the Miniconda installation script will ask you about this.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -p ~/eteconda/
curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh > Miniconda3-latest-MaxOSX-x86_64.sh
bash Miniconda3-latest-MaxOSX-x86_64.sh -p ~/eteconda/
- open a new shell (IMPORTANT!), so you have your new conda env initialized.
- Then create an enviroment to run this tutorial.
conda env create -f course/REQUIREMENTS_conda.yml
conda activate etecourse
pip install -I ete3
# Enter data directory and uncompress data
cd course/data/
tar zxf fasta.tar.gz
tar zxf phylo.tar.gz
tar zxf evol.tar.gz
# Start jupyter in the root directory of this repo
cd ../
jupyter notebook