Pylogeny

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It would be great to get Pylogeny working with Python3: - Remove dependency on mysqldb-python - Perhaps use [mysqlclient](https://github.com/PyMySQL/mysqlclient-python) as a drop-in replacement that works for both Python2 and Python3...

sdwfrost

Is there a way to specify a substitution matrix when calculating the likelihood of a tree? I am using amino acid data as a test set and would like to...

jba462

[A possible resource.](http://plindenbaum.blogspot.ca/2012/07/parsing-newick-format-in-c-using-flex.html)

AlexSafatli

Can be done with easy interfacing with executable interface in executable.py.

AlexSafatli