Hello all, I see that some of the species under the Prevotella genus have been represented with Clade A, B, and such. I am analyzing some gut microbiome samples, I am finding Prevotella copri clades A through I. Is there any way I can easily map the previous names of these species (any official release), as it is becoming very difficult to find literature with the new names?
Any suggestions are welcome.
Thank you
Vikas
Hi @Vikas
Which database version are you using? Since vJun23 we do not use anymore the “clade A” nomenclature but the NCBI names (e.g. Segatella copri)
Hi @Claudia_Mengoni ,
I had used vOct22 as I was also running humann4 analysis, and humann4 was not working with any versions.
Is there a function in MetaPhlAn where I can convert results from one database version to another? Or do I have to run Metaphlan4 again?
I see, if you want to run humann4 for the moment you have to stick to vOct22. If you are only concerned about the Prevotella names, you can use this tab-separated file of the latest metaphlan (vJan25) which tells you for each SGB which are the taxonomies. For Prevotella clades the SGB number should be the same between vOct22 and vJan25, so you can retrieve the updated taxonomy by using the SGB id.
Ok thank you..
In the vOct22 database, can you please tell me where I can find the SGB list like this?
In the same folder: Index of /biobakery4/metaphlan_databases
