AKRUP

AKRUP: Ancestral Karyotype Reconstruction Universal Pipeline

Author	wangjiaqi
Email	[email protected]
License	BSD

Description

Include "bottom-up" inferences of ancestral karyotypes and "top-down" inferences of ancient chromosome evolutionary trajectories

Installation

• Pypi

  pip install AKRUP
  

The AKRUP requires the following dependencies :

• Python (>3.7) with matplotlib, biopython, click, numpy，pandas, and scipy libraries. Note that the current version no longer supports python 2.

• R with the ggridges, forcats and ggplot2 packages.

• perl with the BioPerl packages.

Dependent third party software that has been integrated：

clustalw2	Larkin et al., 2007
ColinearScan	Wang et al., 2006
blast+	Camacho et al., 2009

Tips

• Default parameters, configuration files and usage instructions for all subroutines of the AKRUP software are provided. Please consult the documentation at the Wiki.

• Detailed user tutorials and test data are provided. Please consult the documentation on AKRUP-example.

• Provides ancestral karyotypes for multiple phylogenetic nodes of monocots. Please consult the documentation on monocots-karyotype-evolution.

Citations

If you use AKRUP for your work, please cite: