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Welcome to the pll-modules wiki! You will find here more documentation material regarding pll-modules. Including, but not limited to, theoretical background, use cases, possible enhancements and a guide on how to contribute to pll-modules.

Contributing to pll-modules

pll-modules follows the same rules as libpll. You can read about pll coding style here: Contributing to libpll

On top of that, a few rules apply to the modular structure.

1. Modules are independent. Apart from algorithm, there must be no dependencies between modules.
2. Whenever a function is updated, related documentation should be updated as well. If it affects test cases or examples, make sure they work properly before pushing.
3. Please consider adding additional test cases, especially for critical functionality.

Download and Install

1. Download the latest distribution at Releases
2. Run ./configure && make && make install

A Beginner's guide to libpll

Modules

Module	Prefix	Description	API
binary	pllmod_bin_	Binary I/O	API Reference
msa	pllmod_msa_	MSA management	API Reference
optimize	pllmod_opt_	Optimization algorithms	API Reference
tree	pllmod_tree_	Tree management	API Reference
util	pllmod_util_	Convenience functions	API Reference
algorithm	pllmod_algo_	High level algorithms	API Reference