SynTracker Version 1.4.0

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.

SynTracker Version 1.3.1

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.

SynTracker Version 1.3.0

Version 1.3.0:
Removed the biopython package from the conda environment file (SynTracker_env.yml).
The new conda environment is named SynTracker_1_3.
The Blast processes are executed now by the Subprocess module directly instead of using the deprecated Bio.Blast.Applications module.

SynTracker Version 1.2.7

Changes in this release:

• 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.

SynTracker Version 1.2.6

The script syntracker.py can now be executed from every path (not necessarily from the directory in which it is located).

SynTracker Version 1.2.5

• Added mode 'continue_all_genomes': start from the reference genomes loop and process all of them again without repeating the blastDB building stage.
• Changed the column names of the genome-specific output files to match the names of the summary output files.

SynTracker Version 1.2.4

Removed sampling sizes of 20 and 30.
Now, SynTracker samples the following number of regions: 40, 60, 80, 100 and 200.

Added printouts to a logfile.

SynTracker Version 1.2.3

Added an option --avg_all, to create additional output table, where the APSS are calculated using all available regions of each pair of samples (in addition to the subsampled tables).

SynTracker Version 1.2.2

The command-line argument --set_seed was removed. By default, a seed=1 is set for the subsampling of N regions per pair of samples to enable reproducibility between different SynTracker runs.
If the user wishes to use no seed for the subsampling, he can use the --no_seed option.

SynTracker Version 1.2.1

The two main R processes (the synteny analysis performed by DECIPHER and the synteny scores calculation) were merged into one function that is executed in parallel for each compared region.