Ancestral Karyotype Reconstruction Universal Pipeline
Project description
AKRUP
AKRUP: Ancestral Karyotype Reconstruction Universal Pipeline
| Author | wangjiaqi |
| wangjiaqiky@163.com | |
| License | BSD |
Description
Include "bottom-up" inferences of ancestral karyotypes and "top-down" inferences of ancient chromosome evolutionary trajectories
Installation
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Pypi
pip install AKRUP
The AKRUP requires the following dependencies :
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Python (>3.7) with matplotlib, biopython, click, numpy，pandas, and scipy libraries. Note that the current version no longer supports python 2.
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R with the ggridges and ggplot2 packages.
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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
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Default parameters, configuration files and usage instructions for all subroutines of the AKRUP software are provided. Please consult the documentation at the Wiki.
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Detailed user tutorials and test data are provided. Please consult the documentation on AKRUP-example.
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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:
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