Update scripts and README.md file to deal with Issue #1

[sabifo4]

Hi Sishuo,

As suggested, here you have a pull request. Below, you can find a list of the steps I followed:

1. Fork your repository.
2. Include the changes that we made to run bs_inBV in your ruby scripts.
3. Update the main README.md file to make it much easier to understand the following:

• Installation procedure (i.e., gems, third-party-tools, changes to code required).
• Usage + Example.
• PAML usage when running MCMCtree with the approximate likelihood calculation.

Once you revise the proposed changes, if you think everything makes sense, you can merge the repos!

All the best,
Sandy

[evolbeginner]

Dear Sandra,

Thanks so much! I will test it soon. meanwhile, i have created a v1.0 release for the previous version.

I think the following is why i thought only "colorize" and "parallel" need to be installed for ruby gems. i will add a testing script on top of your PR. In ruby 3.0+ some of the following have been installed by default (but except for "bio" and "bio-nwk"); I didn't realize the diff ruby versions issue until you pointed it out (not many people use ruby in bioinfo today). any Qs suggestions and Qs pls don't hesitate to let me know. Thanks again!

cheers,
sishuo