PCG
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amnh
𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search
Previously we were statically linking but doing that with `glibc` is a big problem (see [here](https://stackoverflow.com/questions/57476533/why-is-statically-linking-glibc-discouraged)). It is recommended instead to use musl for static linking.
When we read in data files and associate them with a TCM, they inherit the alphabet defined in the TCM file. We need to assert that every symbol found in...
Currently, our "cost" type is a `Double` or a new-typed `Double` labeled `ExtendedReal`. Our use-case for `Cost` does not overlap well with the `Num` and related "numeric" type-class instances. Our...
There is currently a Newick serialization type-class in `pcg-serialize`. We should require that newick serialization place the larger subtree on the right. Additionally, if two subtrees are of equal size,...
If we don't check this, the taxa can be placed anywhere on the tree and will cause problems.
The [user guide](https://downloads.haskell.org/ghc/latest/docs/html/users_guide/runtime_control.html) gives various options for runtime parameters particularly for tuning the garbage collector. We should experiment with changing the allocation area of the program to see if this...
**Issue by [ima-hima](https://github.com/ima-hima)** _Thursday Mar 30, 2017 at 02:40 GMT_ _Originally opened as https://github.com/ima-hima/PCG/issues/17_ ---- - [ ] Add documentations - [ ] Data character blocks (BEGIN DATA) may be...
We currently generate invalid implied alignment. The pre-order traversal of implied alignment algorithm relies on knowing if the current node is the left or right child of it's parent. This...
Experiment with ST, TVars, and HashTable libraries to implement a Haskell-side memoization library for Hashable hashable structures. See if this is more efficient than the FFI binding to C++. We...
__The problem__ Currently our character data is represented as follows: ```haskell newtype ContinuousCharacter = CC (ExtendedReal, ExtendedReal) -- where for the sake of completeness ExtendedReal is defined as: newtype ExtendedReal...