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wyp1125 / MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
http://chibba.pgml.uga.edu/mcscan2/
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Question on missing homologous pairs in the .colinearity file #27

Open Mandyzg opened 4 years ago

Mandyzg commented 4 years ago

Hello,

I have a question regarding the default implementation of MCScanX, As the manual suggested, I first run blastp and obtained the .gff and .blast file that were used as input for MCScan. In the .blastp file, I have noticed gene pairs with alignment e-value as low as 1e-110. However, these matched gene pairs were not shown in the .colinearity file after I run MCScanX. I have read through the manual and the paper, but still couldn't find any explanation for that. Can anyone please clarify?

Thanks in advance, Mandy,

Surbhigrewal commented 9 months ago

Hi @Mandyzg did you work out a solution to this?