# whole-genome-duplication

**Repository Path**: dingfun/whole-genome-duplication

## Basic Information

- **Project Name**: whole-genome-duplication
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 1
- **Created**: 2020-06-16
- **Last Updated**: 2021-07-12

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README


# Whole-genome-duplication


Pipelies for genome analysis of *Schizothorax o’connori*, a endemic fish in Tibet; 

Schizothoracinae (order Cypriniformes, family Cyprinidae) is an important subfamily of endemic fish on the

QTP.Whole-genome duplications (WGDs) of Schizothoracinae are believed to have played a significant role in 

speciation and environmental adaptation on the Qinghai-Tibet Plateau (QTP). 

  ![*S o’connori*](https://github.com/DingDingFan/whole-genome-duplication/blob/master/Fish.png) 



It contains 4 part:


  ## 1  WGD_subgenome_split

    Split the sub-genome generated by WGD.

  ## 2  Ohnolog

    Detect Ohnolog genes generated by WGD.

  ## 3 Gene_Lost

    Desinged to find singleon genes after WGD.

  ## 4 LASTZ_alignment_visualize

    LASTZ aligment visualization with genes structure and repeat element ! 


## Dependance

  You can install all dependence with conda:
  
  ```
  conda install -c bioconda lastz
  conda install -c bioconda last
  conda install -c conda-forge perl
   
  ```

UCSC userApps can be found on :

http://hgdownload.cse.ucsc.edu/admin/exe/


## Contact

  Details can be found on the correspongding dirment;

  If have any problem and improvment ,please contact to biocomfun@qq.com


## End