mitos 1.1.7

MITOS

These 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.

Usage on Galaxy

MITOS should primarily be used via Galaxy. It is available for instance on usegalaxy.eu

• MITOS2
• MITOS

Installation

There are three ways to install. Preferred 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 --strict-channel-priority -c conda-forge -c bioconda -n mitos
   • this will install MITOS2. For MITOS use conda install "mitos<2" --strict-channel-priority -c conda-forge -c bioconda -n mitos
   • in case of problems with resolving environments try to use use --solver libmamba or replace conda by mamba.
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

From runmitos.py help:

mandatory options:
  -c CODE, --code CODE  the genetic code
  -o OUTDIR, --outdir OUTDIR
                        the directory where the output is written
  --linear              treat sequence as linear
  -r REFDIR, --refdir REFDIR
                        the directory where the reference data is found

Please note that the reference data for the -r flag needs to be downloaded from Zenodo (MITOS, MITOS2).

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