Welcome to PoMo’s documentation!

Implementation of a polymorphism aware phylogenetic model using HYPHY.

Created by:
  • Nicola De Maio
  • Carolin Kosiol
  • Dominik Schrempf

For a reference, please see and cite: De Maio, Schlotterer, Kosiol (MBE, 2013), and/or: De Maio, Schrempf and Kosiol (in preparation). You can use this software for non-commercial purposes but please always acknowledge the authors.

Feel free to post any suggestions, doubts and bugs.


PoMo comes with a small python package libPoMo. It contains several modules that ease the handling and preparation of data files in variant call format (vcf), fasta format and counts format (cf).

This documentation focusses on this library. For a general introduction to PoMo, please visit PoMo at github.com. If you only want to convert file formats, you are invited to use prepared scripts than come together with PoMo on github.

The libPoMo package is split into the following modules:
  • main: Contains functions that are used by PoMo.
  • seqbase: Provides basic functions and classes needed to work with sequence data.
  • fasta: Provides functions to read, write and access fasta files.
  • vcf: Provides functions to read, write and access vcf files.
  • cf: Provides functions to read, write and access files that are in counts format.

Indices and tables