ConvPhaseGui

Reconstruct haplotypes from sequence data. Input and output can be in TSV or FASTA format.

This is a Qt GUI for ConvPhase, a convenient phase program that combines PHASE and SeqPHASE.

Executables

Download and run the standalone executables without installing Python.

Installation

ConvPhaseGui is available on PyPI. You can install it through pip:

pip install itaxotools-taxi-gui
convphase-gui

Usage

For information on how to use the program, please refer to the 1st section of the Hapsolutely manual.

Packaging

It is recommended to use PyInstaller from within a virtual environment:

pip install ".[dev]" -f packages.html
pyinstaller scripts/convphase.spec

Citations

ConvPhaseGui was developed in the framework of the iTaxoTools project:

Vences M. et al. (2021): iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists. - Megataxa 6: 77-92.

Sequences are phased using PHASE and SeqPHASE:

Stephens, M., Smith, N., and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978--989.

Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics, 73:1162-1169.

Flot, J.F. (2010) seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments. Mol. Ecol. Resour., 10, 162–166.