Hello Andreas,
I made contact with PyloPthias article maintainer as u said and he said he will make contact the main developer (and be pleased about it :) ) to make program codes more understandable and packable for debian standarts.
I made contact with them 2 days ago wait response for now.
I look at some documentations and packages you advised me (fastqc, exonerate, seaview, gubbins, swarm-cluster, dindel, murasaki) but there is some clearness i came across you advise these packages to me for example or making test suites and what we are testing ? Are we test the packages for succesfully building and installing or functionality.
I look exonerate etc. and couldn't find any debian/tests directory i am confused.
In conclusion i understanded i must study more about it and i can use MoM for help . Thank you for help.
Best Regards