Ashton Pooley issues

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                                            Ashton Pooley

Utilize os.path.join instead of concatenation

This pull request addresses the issue raised in [this issue](https://github.com/uym2/TreeShrink/issues/41)

IndexError due to double backslash windows directories.

Due to Windows using double backslash and the recursive list dir function assuming directories use a single forward slash the following exception is caused during installation `Traceback (most recent call...

TypeError when trying to initialise Alignment object using positional argument.

Hello, I'm attempting to run a profile alignment using two sub alignments stored as string in memory. In order to do so I am initialising a new Alignment object using...

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