Zach

Hi Pasi, Thanks so much for your response. I haven't tried plotting a Marey map, as the genome I am working with is scaffold-level. I tried OrderMarkers2 without grandparentPhase and with proximityScale=100, and that has made a huge difference. Now only one out of 18 linkage groups has any error-indicating red lines in the LMplot output, whereas before it was most of the linkage groups. I tried adding grandparentPhase while running evaluateOrder on these ordered maps, and the likelihood score dropped,...

Hi Pasi and Lep-Map3 community, Thank you for this excellent software and your commitment to answering questions from users. I am looking for advice on how to resolve some concerning LMplot output (see attached). Any explanations you could provide for what these plots are indicating would be very helpful. I understand the red lines indicate errors, but I am unsure how to interpret what these errors mean exactly and what could be causing them. I am also attaching code I used to generate these linkage...