docs: adds extra CLI examples for outputing newick format

README.rst

@@ -273,6 +273,25 @@ Validating a list of TaxIDs against a Tree data structure in ``pickle`` format:
   taxonomy-resolver validate -in tree.pickle -taxids testdata/taxids_validate.txt
 
 
+Load a previously built Tree data structure in ``pickle`` format and search for one or more TaxIDs (for example human, TaxID '9606'). Included, excluded and filter lists can be optionally passed as shown above.
+
+.. code-block:: bash
+
+  taxonomy-resolver search -in tree.pickle -taxid "9606" -out testdata/taxids_human.txt
+
+Writing the 'complete' human sub-tree (i.e. all levels of the hierarchy) in ``newick`` format can be done via the build command and passing a TaxID filter file, which can be generated by running the search command shown previously.
+
+.. code-block:: bash
+
+  taxonomy-resolver build -in tree.pickle -inf pickle -taxidsf testdata/taxids_human.txt -out testdata/taxids_human.nwk -outf newick
+
+Alternatively, ``newick`` output can be generated for the 'local' human sub-tree (i.e. species and sub-species levels only), directly using the search command, as shown below:
+
+.. code-block:: bash
+
+  taxonomy-resolver search -in tree.pickle -taxid "9606" -out testdata/taxids_human_local.nwk -outf newick
+
+
 Contributing
 ============