MCScanX
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wyp1125
MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
I am a PhD student doing a collaborative project between Trinity College Dublin and UCLondon and am using MCScanX. I am just getting to know the tool and have been...
Hi Yupeng, Thanks for making MCScanX available. I'm trying to run the tool on my concatenated blast results and "gff" but I keep getting 0 matches imported and 0 discarded....
I have tried to use the sample data and it doesn't seem to work? Perhaps I am doing something wrong but I seem not to be able to get any...
 Hi, I was using MCScanX, thanks for your contribution to this marvelous software. But I found a little problem that the order of column might be mistaken that would...
How should value of epoch number be specified for MC-ScanX runs? Will it change depending on the taxonomic / phylogenetic distribution of species being analyzed: within genus vs across genera...
Hi, i downloaded the zip file from git hub and followed instructions, after make command i received this error: ``` g++ struct.cc mcscan.cc read_data.cc out_utils.cc dagchainer.cc msa.cc permutation.cc -o MCScanX...
hello, I am preparing the inputs for MCScanX and I find this incongruence: you say you want a .bed file, but the format you give in the readme is different:...
Hi, thanks for developing MCScanX! I've found it of great use. I have already ran one analysis using the -a option to stop after writing the .collinearity file, but now...
Hi, thank you for developing MCScanX. I wonder if it is possible to use output of blastn instead of blastp for the analysis. I have a huge genome encountering many...
Hey, I got a quick question about the e-value cutoff for collinear genes. For example, here is a list of syntenic blocks. All the genes have very low e-value from...
