Determine horizontal transfer candidates based on sequence similarity.
Blast2hgt also provides:
- A strategy for balanced sequence sampling from each taxonomy group to reconstruct phylogenetic trees.
- Scripts for semiautomated sequence extraction (based on Blast2hgt outputs) and phylogenetic analyses.
The query objects can be proteins, genes or partitial genomic sequences.
Note: A MySQL database of BLAST hit's IDs and their species taxonomy is required:
- If the BLAST database is nr, you have to import the nr sequence IDs and their taxonomy IDs into the MySQL database (use
import_nr.acc.taxid.sql). - If the nt is blasted, the nt sequence IDs and their taxonomy IDs should be imported.
See Blast2hgt_manual.pdf for detailed guidelines.
If you find these codes useful, please cite:
Li, M., Zhao, J., Tang, N., Sun, H., & Huang, J. (2018). Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis. Frontiers in Plant Science, 9, 701. https://doi.org/10.3389/fpls.2018.00701