syntR is an R package for the reproducible identification of synteny blocks and chromosomal rearrangments via comparison of two genetic maps. syntR implements an error-aware clustering algorithm specifically designed for the highly linear structure of comparative genetic map data. syntR can be used to identify synteny blocks using any type of ordered genetic markers.
You can install syntR from Github with:
Find synteny blocks shared between Helianthus petiolaris and Helianthus annus (provided as example data):
# load the syntR library library("syntR") # load data data(ann_pet_map) # convert data to a single ordered scale map_list <- make_one_map(ann_pet_map) # find synteny blocks synt_blocks <- find_synteny_blocks(map_list, max_clust_range = 2, max_nn_dist = 10, plots = TRUE) # print the resulting synteny blocks dataframe synt_blocks[]