Test run using example data

An example set is provided with the UBCG2 package. Please follow the instruction below:

1. Unzip the UBCG2 package. External programs (See requirements in the download page) must be installed and their path must be designated in the programPath file.
2. Example fasta files are in the "fasta" directory. Execute the commands given here to convert fasta files to ucg files.
3. Check the "ucg" directory by entering a command like "ls ucg/" where you will be able to find eight *.ucg files that contain UBCG gene sequences with metadata.
4. Execute the following line in the directory where UBCGtree.jar file exists to align gene sequences and infer the UBCG tree.
   • java -jar UBCGtree.jar align -ucg_dir ucg -run_id my_example -leaf label
5. Outputs will be saved in the "output/my_example" directory
6. Take the "concatenated_gsi(n).nwk" file and open with MEGA or other tree-viewing programs. (The below is the screenshot of MEGA.)

An example UBCG tree. (T) denotes type strain.

This UBCG tree shows that

• Two Streptococcus constellatus subspecies are closely related; all 92 UBCGs (Bacterial core gene set) supported this.
• Streptococcus pneumoniae TIGR4 is closely related to the type strain of Streptococcus pneumoniae; 72 out of UBCGs supported this.
• Two tentatively new species, named CP012646_s and CP014326_s, formed a monophyletic clade with S. pneumoniae, Streptococcus pseudopneumoniae, and Streptococcus mitis.

The below is the dendrogram showing OrthoANI-based clustering of the same genomes. Please note that CP012646_s and CP014326_s represent a novel species using 95~96% average nucleotide identity (ANI) cutoff [Learn more].

OrthoANI UPMGA clustering of the example set.