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I was working with plants and almost never had to load more than 10 genomes in my research. |
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Just computing anchors, and also if possible to get a score for collinear blocks. I am wondering if you can create a distance metric between genomes based on synteny calcualted with MCScanX |
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Computing anchors for should not be a problem. However MCscan is basically setup to only compute "pair-wise" synteny blocks. So it's possible to try comparing all 2800 to a single genome, doing all pairwise will need 2800 * 2800 / 2 comparisons. |
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Another question. These genomes are a pangenome, and I have already created orthologus families for each gene in all genomes. Would it be possible to only run the necessary script to create the collinearity alignment? |
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Can MCScan perform the synteny on a large number of genomes? For instance ~2800 microbial genomes? Is there a computational maximum?
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