Zombi is a flexible platform of genome evolution which can be of great interest to those who want to test different evolutionary hypotheses under simulations and need to use a fast and easy-to-use tool to generate species trees, gene trees or sequences. Zombi's output is especially simple and easy to read, understand and parse.
Zombi current version: Zombi 1.0.1
Added new models! --> Tm, Ts and Ss
Writen by Adrián A. Davín
Using ideas, suggestions and comments coming from: Théo Tricou, Thibault Latrille, Nicolas Lartillot, Vincent Daubin, Damien de Vienne, Eric Tannier and Gergely J. Szollosi
Please, if you have any doubts or need a hand, just contact me here: aaredav@gmail.com
Please, if you use Zombi, cite:
Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages.
Adrian A. Davin, Theo Tricou, Eric Tannier, Damien M. de Vienne, Gergely J. Szollosi
Bioinformatics, btz710, https://doi.org/10.1093/bioinformatics/btz710
First, clone the repository to your computer
git clone https://github.com/AADavin/ZOMBI
Second, you need python 3.6 installed with ETE3, numpy, networkx and pyvolve
pip3 install ete3 numpy networkx pyvolve
You might find some problems when installing the ete3 library, more specifically, when ete3 tries to install the library six. Simply use the command pip3 to install the missing libraries. For instance:
pip3 install six
There is a detailed Wiki that explains how Zombi works here and it takes around 15 minutes of your time reading it! But if you want to launch it right away, just read this.
There are three main modes to run Zombi: T (species Tree), G (Genomes) and S (Sequences)
You must run the computations in sequential order. This means that: Computing genomes requires having computed previously a species tree computed with the T mode. Computing sequences requires having computed previously genomes with the G mode.
The parameters are read from a .tsv file that can be modified with any text editor.
To start using Zombi just write:
python3 Zombi.py T ./Parameters/SpeciesTreeParameters.tsv ./Output_folder
These will generate a Species Tree along with some other files in ./Output folder/T
Then, you can simulate the evolution of genomes in that species tree using:
python3 Zombi.py G ./Parameters/GenomeParameters.tsv ./Output_folder
Make sure that the Output_folder is the same that you were using when you generated the Species Tree! Zombi will simulate the evolution of genomes inside the whole species tree and it will print a very detailed information about them in ./Output folder/G
Then, you can simulate the evolution of sequences for each gene in that species tree using:
python3 Zombi.py S ./Parameters/SequenceParameters.tsv ./Output_folder
Zombi is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
Zombi is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. http://www.gnu.org/licenses/.