phylogeny for similar consensus sequences

Question

[vmicrobio]

Hi,

I'm looking for a software to do phylogenic trees from related consensus sequences of viruses.

I have already tried realphy and nextstrain. I don't know if Realphy is still curated and Nexstrain seems specific to covid.

I also tried snpiphy which is very good but using one fasta reference and fastq files (I want to compare my data to several consensus references).

Have you any advice/recommendations about other softwares to do that?

Thanks

Answer 1

[Ali May]

If you select an appropriate reference (R) that is closely related to both your data (D) and the sequences you want to compare to (S), you should be able compare D to S by querying them together against R using a tool like snpiphy.