I have multiple lists of species names generated from BLAST for different proteins, and I want to retrieve each list's phylogenetic relationships from a universal common tree for all species.
1) May I know if this was how the NCBI Common Tree generated? (Where we input a list of species names, and it extracts the relevant nodes from a common universal tree.)
2) If the NCBI Common Tree is generated from a universal common tree, may I know if there is a way to use the NCBI Common Tree tool from the command line?
3) If the NCBI Common Tree is not generated from a universal common tree, could you kindly point me to resources where I can do this?
Any input would be greatly appreciated, thank you! :)