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Update README and citation section (#677)
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* don't make index

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tanghaibao authored Jun 13, 2024
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# JCVI utility libraries

[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.31631.svg)](https://doi.org/10.5281/zenodo.594205)
[![Latest PyPI version](https://img.shields.io/pypi/v/jcvi.svg)](https://pypi.python.org/pypi/jcvi)
[![bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/jcvi/README.html?highlight=jcvi)
[![Github Actions](https://github.com/tanghaibao/jcvi/workflows/build/badge.svg)](https://github.com/tanghaibao/jcvi/actions)
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| Email | <[email protected]> |
| License | [BSD](http://creativecommons.org/licenses/BSD/) |

## Citations
## How to cite

- If you use the MCscan pipeline for synteny inference, please cite:

_Tang et al. (2008) Synteny and Collinearity in Plant Genomes. [Science](https://science.sciencemag.org/content/320/5875/486)_
> [!TIP]
> JCVI is now published in iMeta!
>
> _Tang et al. (2024) JCVI: A Versatile Toolkit for Comparative Genomics
> Analysis. [iMeta](https://doi.org/10.1002/imt2.211)_
![MCSCAN example](https://www.dropbox.com/s/9vl3ys3ndvimg4c/grape-peach-cacao.png?raw=1)

- If you use the ALLMAPS pipeline for genome scaffolding, please cite:

_Tang et al. (2015) ALLMAPS: robust scaffold ordering based on multiple maps. [Genome Biology](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0573-1)_

![ALLMAPS animation](https://www.dropbox.com/s/jfs8xavcxix37se/ALLMAPS.gif?raw=1)

- For other uses, please cite the package directly:

_Tang et al. (2015). jcvi: JCVI utility libraries. Zenodo. [10.5281/zenodo.31631](http://dx.doi.org/10.5281/zenodo.31631)_

![GRABSEEDS example](https://www.dropbox.com/s/yu9ehsi6sqifuaa/bluredges.png?raw=1)

## Contents
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