Add print statements.

[iamciera]

For the command line version. There are many things that need to be printed.

• Like make sure the user is inputting alignment files. Maybe just checking if the files have "-" and print out if the sequences are NOT alignments. Or just print how many files and what type of files are read in
• error messages (like "this is not a fasta file"
• success print statement and tell user where output file is located.

[iamciera]

Only task left is printing out if the sequences are alignments or not.