Tomas Flouri

Document the following in the wiki: - Invariant sites (theory behind + usage) - Ascertainment bias (theory behind + usage) - Derivatives computation (theory behind + usage) - `attributes` partition...

Important documentation regarding libpll

1

I'd like to keep a list of important libpll peculiarities which the users should be aware of. If you feel that certain points should be given special emphasis in the...

Change of data types

11

Perhaps now it would be a good idea to decide the data types of the following `pll_partition_t` variables: | **type** | **Variable** | **Role** | Suggested type | | ---...

Coverage tests

1

Compile `libpll` with `gcc --coverage` and use `gcov` to detect which parts of `libpll` are not tested by the testing framework. I intend to do this end of december.

Adapt fast randomized stepwise addition for unrooted trees to work with three sets of vectors per node

1

Memory requirements will increase, but we won't need to do any re-computation when iterating a tip through all possible placements (edges).

Document testing framework

1

Document in the [wiki](https://github.com/xflouris/libpll/wiki) how to customize the testing framework, e.g. disable memory checks, execute specific tests using wildcards, speed tests, specific architectures

Check const correctness and use restrict keyword

2

Add `const` to function parameters where it would make code more readable. Use `restrict` keyword to limit pointer aliasing.

Implement AVX vectorized exponentiation

1

Implement `_mm256_exp_pd()` for computing transition probability matrices (Issue #105 ) The intrinsic does not map to an instruction and is only available in the [Intel Small Vector Library](https://software.intel.com/en-us/node/583228). There exists...

Document the following: - p-matrix computations (theory + usage) and how pmatrix updates work (rate matrix specification for each rate category) - Document the `PLL_ATTRIB_PATTERN_TIP` attribute, and the various maps...