Welcome to the documentation of cflib!

This library provides functions and classes to handle file conversion between standard formats (e.g., fasta or VCF files) to counts files that are used by IQ-TREE with PoMo, and implementation of a polymorphism aware phylogenetic model.

Created by:
  • Dominik Schrempf

For a reference, please see and cite: Schrempf, D., Minh, B. Q., De Maio, N., von Haeseler, A., & Kosiol, C. (2016). Reversible Polmorphism-Aware Phylotenetic Models and their Application to Tree Inference. Journal of Theoretical Biology, in press.

Feel free to post any suggestions, doubts and bugs.


cflib contains several modules that ease the handling and preparation of data files in variant call format (vcf), fasta format and counts format (cf).

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