How to get initial tree with ete3

You can use python package ete3 and run this in python. Note that ete3 is already installed in fastoma environment.

Example when you want to find the tree for a list of species with these taxanomic IDs

list_tax=["2777116", "135651" ,"6239", "2018661", "96644"]

from ete3 import NCBITaxa
ncbi = NCBITaxa()

list_tax=["2777116", "135651" ,"6239", "2018661", "96644"]

taxid2name = ncbi.get_taxid_translator(list_tax)
print(taxid2name)
list_sp= list(taxid2name.values())

#tree = ncbi.get_descendant_taxa(list_sp, collapse_subspecies=True, return_tree=True)
tree = ncbi.get_topology(list_tax)
tree.write()

#print tree.get_ascii(attributes=['sci_name', 'taxid'])
node_tax=[]
for  node in tree.traverse():
    node_tax.append(node.name)
node_tax.append(tree.name)

taxid2name = ncbi.get_taxid_translator(node_tax)
for  node in tree.traverse():
    node_name=node.name
    node.name="_".join(str(taxid2name[int(node_name)]).split(" "))
tree.write(format=1,format_root_node=True)

The output will be

{6239: 'Caenorhabditis elegans', 96644: 'Mesorhabditis spiculigera', 135651: 'Caenorhabditis brenneri', 2018661: 'Diploscapter pachys', 2777116: 'Caenorhabditis auriculariae'}
'((Caenorhabditis_brenneri:1,Caenorhabditis_auriculariae:1,Caenorhabditis_elegans:1)Caenorhabditis:1,Mesorhabditis_spiculigera:1,Diploscapter_pachys:1)Rhabditidae:1;'

You can change this python script to start with species name. See here for details.