Phylogeny Tree based on SILVA classification

Question

[neutrinoscientist]

Hello, have a list of species (taxa) and i want to generate a phylogeny tree using SILVA. How to do this? any help please. Thanks.

Answer 1

[Chirag Parsania]

There are multiple ways you can do this. You can directly download the tree given by silva (.tre files)and then filter taxonomy of your interest. However, in the SILVA taxonomical tree, the ids given are silva_id. Therefore, you have to manually map the species name to silva id and then you can extract it. It is very important that from where you get the species id. Otherwise it won't match with the silva species name.

Second option is, you download rRNA sequences for the species of your interest from SILVA given rRNA fasta files. Once you get rRNA sequences, you process them by yourself to create a species phylogenetic tree