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KennthShang / PhaBOX

Local version of the virus identification and analysis web server (tool set)
https://phage.ee.cityu.edu.hk/
Academic Free License v3.0
37 stars 5 forks source link

different results between phagcn2 and phabox #16

Closed mengyuan-JI closed 1 month ago

mengyuan-JI commented 5 months ago

Hi，I use phagcn2 and phabox to do the classification for the same fasta files, but it shows me very different result，Im not sure which one can be trust

KennthShang commented 5 months ago

Hi there,

PhaGCN2 is designed for all viruses. PhaBOX will only predict the bacteriophages.

Best, Jiayu

mengyuan-JI commented 5 months ago

thank you for answering! can I use PhaBOX also for archaea phages?

KennthShang commented 5 months ago

The name archaea phage is not very precise; in most cases, we call them archaea viruses. If you want to predict the taxonomy, then PhaGCN2 should be used. However, if you want to predict the host for them. Cherry_single.py in PhaBOX can be run because CHERRY is designed for all the prokaryotic viruses.

Best, Jiayu

mengyuan-JI commented 5 months ago

I mainly want to make predictions about phages in soil systems, but for example for the contigs "DP_phages_080", phabox gives me: Chaseviridae,1.0 and phagcn2 givesme: Autographiviridae_like. Both of them are bacteria virus.

KennthShang commented 5 months ago

In this case, you should use phabox's prediction. Since I am not correspondence to maintaining PhaGCN2, I am not sure whether they have updated the ICTV taxonomy. But in the case of PhaBOX can give a result, it should have the highest confidence, since we have updated the program regularly.

Best, Jiayu

mengyuan-JI commented 5 months ago

OK，thanks a lot

KennthShang commented 1 month ago

Hi there,

The PhaBOX is upgraded to a 2.0 version with more powerful usage. Besides, it can handle all kinds of viruses now. Feel free to check!

Best, Jiayu