Replace the function names in R/tree.R

[Seyi007]

          [R/tree.R](https://github.com/JRaviLab/MolEvolvR/blob/main/R/tree.R)

Original	Modified	User Facing
convert_fa2tre	convertFA2Tree
generate_trees	convertAlignment2Trees
generate_fa2tre	convertFA2Tree

Originally posted by @the-mayer in #7 (comment)

All updates should follow this format:

Original	Modified	User Facing
original_function	newFunction	✅

NOTE: Before beginning to work on a particular file, please check to see that @jananiravi has given the 👍 on the comment.

Please follow the contributing guidelines and create a new branch containing your changes. Commit your work, and submit a PR when ready for review.

Additionally, use the search in all files functionality in VS code, Rstudio, or any other text editor, and list all files the function is being called or used to be updated later.

[teddyCodex]

@jananiravi okay to go ahead with this?

[jananiravi]

made minor modifications -- go ahead.

[teddyCodex]

@jananiravi You edit above has:

convert_fa2tre --> convertFA2Tree
generate_fa2tre --> convertFA2Tree

is this intentional?

note: using createFA2Tree pending your response.

[jananiravi]

good catch -- intentional because they should have that name but creating duplicate names was not intentional! They both do the same thing (takes fasta sequences and generates trees, but use different algorithms -- that needs to be clarified. Also, I'm not sure which one is in use. Could you check, @the-mayer @epbrenner & recommend accordingly?