mitos 1.0.1

MITOS

Thes are the mitogenome related sources including MITOS and other (more or less) helpful tools. Note that some of the tools are unfinished and not in a production state.

Clearly this README is a stub. We are happy to extend the documentation on request. So just send a message if you need further information.

Installation

There are three ways to install. Prefered is the installation via conda since this also takes care of non-python requirements of the main mitos script.

1. via conda: conda install mitos -c bioconda -m -n mitos

2. via pip: pip install mitos

3. manual: pip -r requirements.txt

For the non-python requirements see README.MITOS.

MITOS

• runmitos.py: standalone CLI MITOS

see also mitos.py –help README.MITOS

genbank file handling

• refseqsplit:

  • splits a file consisting of concatenated gb files into single genbank files

  • its possible to apply filters (taxonomy, prefix)

skewness related programs

• skew:

  compute skewness values for a gene of given genbank files

• skewcum:

  compute cumulative skewness for given genbank files

• skewsvm:

  do svm classification of skewness values .. and try to relate misclassifications to rearrangements

MISC

• gcpp

  • pretty print and compare genetic code