ETE_code.txt

# downloading ETE documentation: http://etetoolkit.org/download/
# build tool documentation: http://etetoolkit.org/documentation/ete-build/

# code works the best with Mac OS X system

# it's recommended to use conda to install ETE:

1. conda create -n ete3 python=3
2. conda activate ete3
3. conda install -c etetoolkit ete3 ete_toolchain
4. ete3 build check

# this activates the conda enviroment to use ete3
conda activate ete3

# build function builds the tree
# (-w) gene tree workflow
# (-a) amino acid FASTA file
# (-n) nucleotide FASTA file
# (-o) output file for tree
5. ete3 build -w standard_fasttree -a NUP62.aa.fa -o output_tree 


# ETE can also be downloaded without using conda:
-- we used this method to download on the class server

#1. in ubuntu, mint and other Debian based distributions
sudo apt-get install python-numpy python-qt4 python-lxml python-six

#2. Install/Upgrade ETE using PIP
pip install --upgrade ete3

#or using EasyInstall
easy_install -U ete3

#or from the sources: Download latest version from PyPU and execute:
python setup.py install 

#3. Compile external tools - optional step, required only by ete-build and ete-evol
ete3 upgrade-external-tools