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).
It contains 4 part:
Split the sub-genome generated by WGD.
Detect Ohnolog genes generated by WGD.
Desinged to find singleon genes after WGD.
LASTZ aligment visualization with genes structure and repeat element !
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/
Details can be found on the correspongding dirment;
If have any problem and improvment ,please contact to biocomfun@qq.com