I am trying to construct ancestral chromosomes using ANGeS for 8 plant genomes, and having problems with the input marker file. I have Orthofinder output as well as MCscan and trying to combine the outputs to get the Marker file as shown in the examples of the software. The problem is the the collinearity blocks (from MCscan) are for pairs of genomes and not for all the 8 genomes, and preparing the blocks based on orthologs (from Orthofinder output) makes the blocks too short for ANGeS. I use R and command line to change the formats usually. Has anybody here had the same experience and could show me the way?