No links between what is displayed when making the json

[alanwang03]

Hi all,

I am trying to test AliTV with your test chloroplast data and my own mitochondrial data (Both only have two species for comparisons). When I tried the chloroplast data, it worked, displaying a link between the two species. However, when I switched to the mitochondrial data with the same script, there was no link (blank) between the two species. The yml and other files were all the same, but the only difference we saw was that there were more link features in the chloroplast. Does anyone know what is going on?

Thank you

[iimog]

If there are no links at all, even though the sequences should be similar then probably something went wrong in the lastz alignment. A common problem is: if the sequences in the fasta files are in lowercase letters, they are treated as masked (see https://github.com/AliTVTeam/AliTV-perl-interface/blob/master/doc/alitv.md#section-genomes).

If this is not your problem, I need more information to figure out what's going on. How did you create the json file (give the command you used)? Are you able to share the fasta, json or log files?