- Suitable for phylogenetic analysis of metazoa
- Phylogenetic representativeness of the sample confirmed
MeMitDB (Metazoan Mitchondrial DataBase) is an open database of curated mitochondrial genomes. This is a completely open source project, following the reproducible research principles; anyone can get copy or contribute.
Aim of the database is the collection of as much as possible different mitochondrial genomes in the same place, following standardized rules for annotations and retrieving. Therefore, publicly available sequences were downloaded from GenBank, filtered, and parsed in order to eliminate redundancy. Basic statistics of a given subset of sequences can be computed directly online, while for thorough analyses all sequences are easily available for download in FASTA format. Many filtering option are available in order to make selection quick and easy.
The pipeline of populating MetMitDB is entirely automated thanks to several Python scripts (available in this repository), which is essential in order to efficiently update and keep the database alive.
The date of the last update was 2016 February, 16.
All data collection was done with workbook.ipynb file, which can be run through ipython server. To run ipython server you can use script start_ipython_notebook_server.sh or just type
ipython notebook --pylab=inline
to run it
To get the database without taxonomical data, donwload it from Yandex.Disk
mkvirtualenv metmitdb
pip install -r requirements.txt
python metmitdb.py