Prep for PyPI

Author: Benjamin-Lee

README.md

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 # Python Codon Adaptation Index
+=======
+# CAI.py: Python Codon Adaptation Index
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 An implementation of Sharp and Li's 1987 formulation of the codon adaption index.
 
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 ## Usage
 ### Simple Usage
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 The simple
+=======
+The simplest way to calculate the CAI of a sequence is to call `CAI()` with the sequence as the first (required) argument and with the `sequences` argument included. The sequences argument is a list of reference sequences. Determining which sequences to use as the reference set is left to the user.
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 ```python
 
 from CAI import CAI
 
 print CAI("ATGGATTAC...", sequences=["ATGTTTGCTAAA", "ATGCGATACAGC",...])
 
-```
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+```
+=======
+```
+### Advanced Usage
+If you have already computed the weights or RSCU values of the reference set, you can supply `CAI()` with one or the other as arguments. They must be formatted as a dictionary and contain values for every codon.
+
+To calculate the RSCU without calculating the CAI, you can use `RSCU()`. `RSCU()`s only required parameter a list of sequences.
+
+Similarly, to calculate the weights of a reference set, you can use `relative_adaptiveness()`. `relative_adaptiveness()` takes either a list of sequences as the `sequences` parameter or a dictionary of RSCUs as the `RSCUs` parameter. 
+
+### Other Genetic Codes
+
+All functions in CAI support an optional `genetic_code` parameter, which is set by default to 1 (the standard genetic code). You may set it to any genetic code within [gc.prt](/gc.prt). 
+
+## Contributing
+Feel free to contribute, open issues, or let me know about bugs. Anything is welcome!
+
+## Contact
+I'm available for contact at [benjamin_lee@college.harvard.edu](mailto:benjamin_lee@college.harvard.edu).
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