This full release fixes some issues of the version 1.2, most important is cleared output of part A for better handling in Geneious, better description of Geneious usage and automated removal of putative plastid sequences in part B.
Notice
- Download 
sondovac-1.3.zip, do NOT downloadSource codeas it does not contain all needed files to run Sondovač. - Unpack 
sondovac-1.3.zipand start in command line bysondovac_part_a.sh -hand by reading documentation. - In case of problems, feel free to open an issue and/or request.