Same chromosome comparison

[Adele-Desmazieres]

Hello,

The number of anchorpoints in same-chromosome comparison is way lower than the number of genes in the chromosome, although blastp computes the similarities between each gene with itself.

Why does the diagonal show a low number of anchorpoints in this plot? (There is 40 anchropoints for MD01-MD01, 5 anchorpoints for MD03-MD03...) Is this behavior expected from i-ADHoRe? I guess it isn't, according to the Figure S3 from the publication Phylogenetic reconstruction based on synteny block and gene adjacencies:

So what am I doing wrong?

Here are the parameters I used:

blast_table = tmp/blast/all_vs_all.txt

output_path = tmp/iadhore/

tandem_gap = 3
alignment_method = gg2
gap_size = 30
cluster_gap = 35
q_value = 0.75
prob_cutoff = 0.01
anchor_points = 5
level_2_only = true
number_of_threads = 7

genome = Prunus_persica
Pp01 tmp/data/PP_lst/Pp01.lst
Pp02 tmp/data/PP_lst/Pp02.lst
Pp03 tmp/data/PP_lst/Pp03.lst
Pp04 tmp/data/PP_lst/Pp04.lst
Pp05 tmp/data/PP_lst/Pp05.lst
Pp06 tmp/data/PP_lst/Pp06.lst
Pp07 tmp/data/PP_lst/Pp07.lst
Pp08 tmp/data/PP_lst/Pp08.lst

genome = Malus_domestica
Md01 tmp/data/MD_lst/Md01.lst
Md02 tmp/data/MD_lst/Md02.lst
Md03 tmp/data/MD_lst/Md03.lst
Md04 tmp/data/MD_lst/Md04.lst
Md05 tmp/data/MD_lst/Md05.lst
Md06 tmp/data/MD_lst/Md06.lst
Md07 tmp/data/MD_lst/Md07.lst
Md08 tmp/data/MD_lst/Md08.lst
Md09 tmp/data/MD_lst/Md09.lst
Md10 tmp/data/MD_lst/Md10.lst
Md11 tmp/data/MD_lst/Md11.lst
Md12 tmp/data/MD_lst/Md12.lst
Md13 tmp/data/MD_lst/Md13.lst
Md14 tmp/data/MD_lst/Md14.lst
Md15 tmp/data/MD_lst/Md15.lst
Md16 tmp/data/MD_lst/Md16.lst
Md17 tmp/data/MD_lst/Md17.lst

Thank you!