add README

README.md

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 # GeneMap
 
+GeneMap, A python tool for identifying the mapping of genes between two genomes by multi evidences.
+![Flow chart](https://raw.githubusercontent.com/wjwei-handsome/wwjPic/main/img/20220722001234.png)
+
+## Table of Contents
+
+- [Background](#background)
+- [Install](#install)
+- [Usage](#usage)
+- [Badge](#badge)
+- [Maintainers](#maintainers)
+- [Contributing](#contributing)
+- [License](#license)
+
+## Background
+
+When we have multiple genomes of the same species (or related species), we usually need to identify the gene mapping relationship between the two genomes(Gene A in genome a, mapped to gene B in genome B). We used four alternative evidence, including:
+
+1. RBH
+   **R**eciprocal **B**est BLAST **H**its
+
+   > Despite these and other complication, the identification of reciprocal best hits for gene products is a good first approximation to the identification of orthologues in two or more organisms. It forms the basis for many orthology-finding tools, such as MCL, OrthoMCL and OrthoFinder. It can be carried out by carrying out BLAST+ searches using a short program, and this will be illustrated below.
+
+2. ortholog
+   [OrthoFinder](https://github.com/davidemms/OrthoFinder)
+3. synteny block
+   [McScanX](<https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)>)
+4. crosssmap
+   [minimap](https://github.com/lh3/minimap2)
+   or
+   [AnchorWave](https://github.com/baoxingsong/AnchorWave)
+
+## Install
+
+TODO
+
+```sh
+$ pip3 install GeneMap
+```
+
 ## Usage
 
-```shell
-python3 bin/GeneMap.py -l tests/Zm-B73v5.genelist -d . -q Zm-B73v5 -t Zv-TEO01
+```sh
+$ GeneMap.py -l list.txt -d work_dir -q GenomeA -t GenomeB -o output_prefix
 ```
 
-![hhh](https://raw.githubusercontent.com/wjwei-handsome/wwjPic/main/img/20220722001234.png)
+## Maintainers
+
+[@wjwei-handsome](https://github.com/wjwei-handsome)
+
+## Contributing
+
+Feel free to dive in! [Open an issue](https://github.com/wjwei-handsome/GeneMap/issues/new) or submit PRs.
+
+Standard Readme follows the [Contributor Covenant](http://contributor-covenant.org/version/1/3/0/) Code of Conduct.
+
+### Contributors
+
+Thanks [@songtaogui](https://github.com/songtaogui) for design ideas.
+
+## License
+
+[GPL-3.0](LICENSE) © Weiwenjie