The PhaBOX2 server is in beta test. For large-scale data, you can also try the local version: https://github.com/KennthShang/PhaBOX

Citation

✏️ Citation

The PhaBOX 2.0v has not been formally published in a journal. But if you want to cite our tools, feel free to use the citations listed below:

PhaBOX (The long-term support package) Jiayu Shang, Cheng Peng, Herui Liao, Xubo Tang, Yanni Sun, PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data, Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad101, https://doi.org/10.1093/bioadv/vbad101
Each independent pipeline # PhaMer (virus identification) Jiayu Shang, Xubo Tang, Ruocheng Guo, Yanni Sun, Accurate identification of bacteriophages from metagenomic data using Transformer, Briefings in Bioinformatics, 2022;, bbac258, https://doi.org/10.1093/bib/bbac258 # PhaGCN (taxonomy classification) Jiayu Shang, Jingzhe Jiang, Yanni Sun, Bacteriophage classification for assembled contigs using graph convolutional network, Bioinformatics, Volume 37, Issue Supplement_1, July 2021, Pages i25–i33, https://doi.org/10.1093/bioinformatics/btab293 # Cherry (host prediction) Jiayu Shang, Yanni Sun, CHERRY: a Computational metHod for accuratE pRediction of virus–pRokarYotic interactions using a graph encoder–decoder model, Briefings in Bioinformatics, 2022;, bbac182, https://doi.org/10.1093/bib/bbac182 # PhaTYP (Lifestyle prediction) Jiayu Shang, Xubo Tang, Yanni Sun, PhaTYP: predicting the lifestyle for bacteriophages using BERT, Briefings in Bioinformatics, 2022;, bbac487, https://doi.org/10.1093/bib/bbac487

In the design of the PhaBOX package, we were inspired by the idea of some methods and we loaded some modules for generating the results.

If we have seen further, it is by standing on the shoulders of giants. We acknowledge these tools and also list the names below::

Diamond Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature methods, 12(1), 59-60.
prodigal-gv Camargo, A. P., Roux, S., Schulz, F., Babinski, M., Xu, Y., Hu, B., ... & Kyrpides, N. C. (2023). Identification of mobile genetic elements with geNomad. Nature Biotechnology, 1-10.
mafft Katoh, K., Kuma, K. I., Toh, H., & Miyata, T. (2005). MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic acids research, 33(2), 511-518.
FastTree Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree 2–approximately maximum-likelihood trees for large alignments. PloS one, 5(3), e9490.

vOTU Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., ... & Kyrpides, N. C. (2021). Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nature microbiology, 6(7), 960-970.
Contamination Nayfach, S., Camargo, A. P., Schulz, F., Eloe-Fadrosh, E., Roux, S., & Kyrpides, N. C. (2021). CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nature biotechnology, 39(5), 578-585. Arndt, D., Grant, J., Marcu, A., Sajed, T., Pon, A., Liang, Y., Wishart, D.S. (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res., 2016 May 3.
Protein annotation Von Meijenfeldt, F. B., Arkhipova, K., Cambuy, D. D., Coutinho, F. H., & Dutilh, B. E. (2019). Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome biology, 20, 1-14.