MCScanX
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wyp1125
MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
Hi, I followed the MCScanX [tutorial](https://github.com/wyp1125/MCScanx#family-tree-plotter-java) and got stuck at this command: java family_tree_plotter -t tree_file -s synteny_file -o output_PNG_file How to create a tree in Newick format? Thank you...
Hello, your software is very good. I saw in your article that the paired homologues that can be analyzed by orthomcl software are used as the input file of MCScanX_h....
Hi, there, I found missing homologs in my results, though they show 100% homolog in my blastp results. I tried different parameters, checked all my command, nothing wrong, and I...
Dr Wang: In the early vserions of MSCanX, the parameter “u” designated the intergenetic distance (defualt value:10kb). This may be true for angiosperms, but recently, we sequenced a fern genome,...
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...
Hello, You mention in the manual that the duplicate_gene_classifier tool should not be used on data from multiple genomes. I could not find the reason why in your paper. Is...
I have done ./MCScanX dir/xyz , and draw a dot.plot successfully with the data produced from ./MCScanX. However , when I draw the fig with circle_plotter program and dual_synteny_plotte ,its...
I got the following error while trying to install MCScanX. Not sure where the problem comes. Hope someone can point out. Thx! yh362@mocha:~/tools/MCScanX$ make g++ struct.cc mcscan.cc read_data.cc out_utils.cc dagchainer.cc...
