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docs/FAQs.md

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+---
+section: FAQs
+icon: material/question
+---
+
+# Frequently Asked Questions
+
+
+### How do I get help?
+The first place to look for help or answers is in here in the documentation.
+You can use the search bar in the navigation to search for terms or function
+names. The next place is in the source documentation strings. Some of the 
+source code is available here in the docs, but the rest can be accessed
+in an interactive environment (e.g., jupyter) by executing a function name
+followed by one or two question marks. The docstrings often contain detailed
+descriptions of parameters and example usage. Finally, you can seek further
+help or advice by raising an Issue on GitHub. To do this, navigate to 
+https://github.com/eaton-lab/toytree/issues and click the green New Issue 
+button in the upper right. Then click on Labels on the right to select 
+"help wanted" or "question" as the category for your issue.
+
+
+### How do I report bug?
+If you believe you have encountered a bug in toytree please let us know by
+raising an Issue on GitHub. To do this, navigate to 
+https://github.com/eaton-lab/toytree/issues and click the green New Issue 
+button in the upper right. Then click on Labels on the right to select 
+"bug".
+
+
+### How can I request a new feature
+We are happy to implement new useful methods in toytree that will help to 
+grow its userbase. To request the implementation of a new method please do so
+by raising an Issue on GitHub. To do this, navigate to 
+https://github.com/eaton-lab/toytree/issues and click the green New Issue 
+button in the upper right. Then click on Labels on the right to select 
+"enhancement". 
+
+
+### How can I contribute to toytree
+We welcome contributors! If you are interested in contributing to toytree
+please first read our contributor's guide. This describes a shared framework
+and style to ensure a cohesive coding style throughout the source code. Then,
+you can raise an Issue on GitHub to indicate the project you are working on.
+This way, you can find if others are already working on the method, or find
+additional contributors for help. To do this, navigate to 
+https://github.com/eaton-lab/toytree/issues and click the green New Issue 
+button in the upper right. Then click on Labels on the right to select 
+"enhancement", and under Assignees, assign your self.
+
+
+<!-- ### ... -->

docs/command-line.md

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+# Command line
+
+
+## `toytree` cli
+Sometimes you might not be in the mood to open a jupyter notebook just to take a quick peek at a tree, in which case, the toytree command line interface (cli) provides a convenient alternative. This tool can be called from a terminal shell to execute one or more simple commands to accomplish tasks such as creating tree drawings, rooting trees, and comparing trees. 
+
+## Subcommands
+Currently three subcommands are supported in the cli: draw, root, and distance. (Please reach out and let us know if you would like to see additional toytree methods implemented in the cli.) Call the help command (-h) to see the available subcommands.
+
+```bash
+$ toytree -h
+```
+
+This will bring up a help statement like below. Each subcommand also has its own help page that describes its usage and options, as demonstrated below.
+
+```bash
+usage: toytree [-h] [-v] {draw,root,distance} ...
+
+toytree command line tool. Select a subcommand.
+
+positional arguments:
+  {draw,root,distance}  sub-commands
+    draw                create tree drawing
+    root                (re)root tree and return to STDOUT
+    distance            compute distance between trees
+
+options:
+  -h, --help            show this help message and exit
+  -v, --version         show program's version number and exit
+
+EXAMPLE: $ toytree draw TREE -ts o -d 400 400 -v
+```
+
+## toytree draw
+
+```bash
+$ toytree draw -h
+```
+
+```bash
+usage: toytree draw [-h] [-ts treestyle] [-d dim dim] [-o basename] [-v [app]]
+                    [-f {html,svg,pdf}]
+                    TREE
+
+positional arguments:
+  TREE               tree newick file or string
+
+options:
+  -h, --help         show this help message and exit
+  -ts treestyle      tree style (default: n)
+  -d dim dim         width height (px) (default: (None, None))
+  -o basename        output basename[.format suffix] (default: /tmp/test)
+  -v [app]           open file with default browser or app. (default: None)
+  -f {html,svg,pdf}  output file format (default: html)
+```
+
+## toytree root
+
+```bash
+$ toytree root -h
+```
+
+```bash
+usage: toytree root [-h] [-o O [O ...]] [-r] TREE
+
+positional arguments:
+  TREE          tree newick file or string
+
+options:
+  -h, --help    show this help message and exit
+  -o O [O ...]  outgroup
+  -r            use regex matching on outgroup string.
+```
+
+## toytree distance
+
+```bash
+$ toytree distance -h
+```
+
+```bash
+usage: toytree distance [-h] [-m {rf,rfi,rfj,qrt}] [-n] TREE1 TREE2
+
+positional arguments:
+  TREE1                tree1 newick file or string
+  TREE2                tree2 newick file or string
+
+options:
+  -h, --help           show this help message and exit
+  -m {rf,rfi,rfj,qrt}  distance metric method
+  -n, --normalize      normalize value between [0-1]
+```
+
+## chaining
+To indicate to the draw function that the NEWICk input is the STDOUT from the previous command, use the `-` character like below.
+
+```bash
+toytree root NEWICK | toytree draw - ...
+```