绘制共线性分析的图片方法有很多,例如:WGDI,MCScanX,JCVI等,本文介绍是是Python版MCScan(JCVI工具包),这个包很强大,是从MCScanx升级而来的基因组共线性分析软件,修改参数还能美化图片,非常方便(如下图所示)。 我们以拟南芥,白菜,甘蓝,油菜四个物种为例,并将油菜分为scaffoldA和scaffoldC,2个基因组,分别分析其他物种...
$ python -m jcvi.compara.catalog ortholog grape peach 20:33:42 [base] lastdb peach peach.cds 20:34:13 [base] lastal -u 0 -P 64 -i3G -f BlastTab peach grape.cds >grape.peach.last 20:34:30 [synteny] Assuming --qbed=grape.bed --sbed=peach.bed 20:34:31 [blastfilter] Load B...
To call synteny blocks, we performed all-against-all LAST [2] and chained the LAST hits with a distance cutoff of 20 genes, also requiring at least 4 gene pairs per synteny block. Chromosome-scale synteny blocks plots were constructed using the python version of MCScan[3]. [1] Tang H, ...
Python 版mcscanx出现AttributeError: 'LayoutLine' object has no attribute 'order'$ python2.7 -m ...
python 版本的MCScanX分析物种之间分共线性时，运行里面的例子时，出现报错信息输入文件有问题吧，你打开...