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Added
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- Added option for identifying parallel and convergent amino acid replacements
for both independent and all branch pairs.
- Added method for identifying divergent amino acid replacements.
- Added ancestral state probability for ASR using CODEML (PAML)
- Added method for identifying parallel, convergent, and divergent amino acid
replacements for sites with probability beyond a specified threshold.
Changed
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- Wrapped empirical amino acid replacement models to a Python module.
- Simplified flags for command line arguments.
Removed
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- Removed text files of empirical amino acid replacements models.