I am trying to find collinear genes between two genomes. I tried using progressivemauve, has anybody used this for this purpose? The program generates a .backbone file which from reading the tool manual and their webpage seems to be the file that contain the collinear information. However, this file just lists the coordinates of the collinear regions from each genome without detail information (such as chromosome information and strand). Can someone who has used the tool comment on this?
I have also tried using mugsy but I am not sure if there is a way to output the identified collinear blocks. From the steps listed in their paper, it seems that the collinear blocks are used to generate the final alignment and the aligned regions are normally huge. So would each huge aligned region consist of multiple collinear blocks?
I am also experiment with i-ADHoRe 3.0 which seems promising. One thing is that the program requires a a list of gene pair homologs obtained from using all-against-all blast that I am still not sure of. Would this be done by blasting my protein fasta sequences from one genome as a query against the other genome?
I will appreciate any feedback on above approaches and suggestions if one approach might be better than the other.