Version 1.4.0:

- Added the script syntracker_makeDB.py to create a blastDB directory, that can be later used in multiple SynTracker runs.
- Added the '-blastDB' command-line argument to use the directory that was created by syntracker_makeDB.py.
- Removed the '--avg_all' command-line argument - this option became default.
 -Fixed a problem in the execution of the 'continue' mode.

Version 1.3.1:

- Removed the option to add metadata file (was not used anyway).
- Added the column 'Ref_genome' to the genome-specific final tables.

Version 1.3:

- Removed the biopython package from the SynTracker_env.yml file
- Changed the execution of Blast processes in blast.py so that Bio.Blast.Applications module (deprecated) is not needed anymore and they are executed directly by the Subprocess module.

Version 1.2.7:

- Removed the flag --save_intermediate
- Changed SynTracker.R so that it writes all the per-region synteny scores objects into files under the R_intermediate_objects folder (always).
  If the user runs SynTracker in continue mode, the regions that were already processed are read from this folder and the synteny analysis (DECIPHER) is performed only on the regions that havne't been processed yet.

Version 1.2.6:

- syntracker.py script can be executed now from every path.
- Move the used R functions from SynTracker_functions.R file to SynTracker.R file to prevent problems if the main python script is executed not from the scripts directory.
- Updated manual and README.

Version 1.2.5:

- Added mode 'continue_all_genomes': start from the reference genomes loop and process all of them again.
 Copy the config.txt file to config_old.txt and write it again without the processed reference genomes.
- Changed the column names of the genome-specific output files to match the names of the summary output files.

Updated manual

Added an option --avg_all, to create additional output table, where t…

…he APSS are calculated using all available regions of each pair of samples.

Removed the set_seed option (when a seed is set, which is the default…

…, it is always 1).

Updated README.md and manual.

Changed version to 1.2.1