PCG
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amnh
𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search
Currently our project can be very painful to build on a fresh machine if it is not easy to grab the correct versions of GHC and cabal. Nix is a...
Ward mentioned that we should add a new build method which uses the distance Wagner. This is described in detail on p. 165 of the Systematics text book. Roughly it...
PCG outputs several data files intended to be consumed by other programs. It would be very nice for the users if we had a script to install all these utilities...
The topological representation should be updated to better represent the phylogenetic forest. Currently we represent phylogenetic DAGs in a newtyped non-empty list to represent a phylogenetic forest. This make it...
Add tree & network versions of TBR, SPR, NNI. Be sure to correct handle forest of components and multi-rooted DAGs. This should be done after the efficient graph editing has...
When running `pcg-test-flu-net` with the following script: ``` read("flu_small_hxnx_hsa_seg1_PB2.fasta") read("flu_small_hxnx_hsa_seg2_PB1.fasta") read("flu_small_hxnx_hsa_seg3_PA.fasta") read("flu_small_hxnx_hsa_seg4_HA.fasta") read("flu_small_hxnx_hsa_seg5_NP.fasta") read("flu_small_hxnx_hsa_seg6_NA.fasta") read("flu_small_hxnx_hsa_seg7_MP.fasta") read("flu_small_hxnx_hsa_seg8_NS.fasta") read("flu_small_poy_edges.tre") build(1,network) report(data,("output.data",overwrite)) ``` it begins by adding a number of network edges but...
When we read a graph we may be given a consensus graph in which nodes can have both multiple parents and multiple children. When we convert this graph into our...
In the new graph representation add a function `validate :: Graph f c e n t -> Bool` which checks that the graph we have is indeed a valid phylogenetic...
Currently character sequences are stored on the nodes of the phylogenetic forest. This make column-wise analysis unwieldy. We should instead store the character sequences as rows in a "character matrix"...
### The various implementations of alignments for dynamic characters. Completion indicates that the implementation has been tested and integrated into a PCG binary. - [x] C DO 2D - [x]...