Update readme and add instructions for installation

[kinow]

Hi,

Thanks for sharing Rootstrap! This PR has the following:

• Adds a requirements.txt with pinned versions (using a range with major.minor versions pinned, leaving patch to latest - semver.org, whenever possible)
• Update README.md using Markdown syntax for code block, with bash as the format
• Update README.md with installation instructions with pip and conda
• Updates the code fixing typos in a function name in rootstrap.py and in a comment
• Removes an unused ML_tree in rootstrap.py
• Fixes a comparison with None using is instead of ==

Using a virtual environment, and running pip install -r requirements.txt after the environment was activated, it installed the dependencies, and the following command worked—as far as I can tell—for me. Though I'm not much familiar with the theory behind it :)

(venv) $ python rootstrap.py tree.treefile tree.ufboot False OG_File1.nex
Note: ingroup taxa are not monophyletic in 0 bootstrap trees

(venv) $ ls -lah tree*
-rw-rw-r-- 1 kinow kinow 2.1K Oct 18 12:37 tree_rooted.treefile # new file, not in git
-rw-rw-r-- 1 kinow kinow 4.8K Oct 18 12:37 tree.rootstrap # new file, not in git
-rw-rw-r-- 1 kinow kinow 2.4K Oct 18 11:51 tree.treefile
-rw-rw-r-- 1 kinow kinow 1.3M Oct 18 11:51 tree.ufboot

• Adds a Dockerfile to easily use the script without installing the dependencies

I was going to add a Dockerfile too, to make it easier to use the scripts without having to install dependencies, but ran out of time, sorry.

Thanks!
Bruno