ordering and orienting scaffolds within linkage group

[LyingToForget]

hi, guys,

Currently, we are trying to anchor genome assembly scaffolds onto pesudo-chromosomes based on a linkage map, which was derived from RAD-Seq technology. We has already mapped markers onto the scaffolds using epcr,

Does any one can suggest us a suitable tools, which can visualize the mapping result within linkage groups and help us ordering and orienting the scaffolds?

what's more, we found quite a bit of markers on a certain scaffold have different order within linkage group and scaffold, although the linkage distance between those marker wasn't too large. Has any one faced the same thing?

[jimmybee]

Whats the organism? Is the genome assembly the exactly the same as the linkage map?

[LyingToForget]

We just know it is A PLANT under the order of “Lamiales”, and, YES, the genome assembly and the linkage map are exactly associated with the same species.