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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

Taxonomy classification: PhaGCN 2.0 vs PhaBOX #20

Closed JialinHe0o0 closed 1 month ago

JialinHe0o0 commented 4 months ago

Hi, Thank you so much for creating such a great tool! When I was doing phage taxonomy classification, I got different results with PhaGCN2.0 vs. PhaBOX's PhaGCN. Your article suggests that PhaGCN 2.0 has higher accuracy than the previous version. So would you recommended to use PhaGCN2.0 for classification and other tools in PhaBOX for host prediction etc? Thank you!

KennthShang commented 4 months ago

If you only want to predict the taxonomy for phages, you can go through and use all the tools in the PhaBOX. The programs are continuously maintained and we have already updated the PhaGCN in PhaBOX to have the latest best performance. ( However, we cannot update the published paper to inform the users

But If you want to predict taxonomy for other viruses, you should go for PhaGCN 2.0. The PhaGCN in PhaBOX only consider the phages sequences in your data.

Best, Jiayu

JialinHe0o0 commented 4 months ago

If you only want to predict the taxonomy for phages, you can go through and use all the tools in the PhaBOX. The programs are continuously maintained and we have already updated the PhaGCN in PhaBOX to have the latest best performance. ( However, we cannot update the published paper to inform the users

But If you want to predict taxonomy for other viruses, you should go for PhaGCN 2.0. The PhaGCN in PhaBOX only consider the phages sequences in your data.

Best, Jiayu

Thank you so much for replying so quickly! It helped me a lot! Best wishes for your work~

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