Comments (1)
Tests made with
import dendropy
tree_list = dendropy.TreeList.get(file=open("data/DS1.subsampled.t", "r"), schema="nexus")
tree_list.write(file=open("data/DS1.subsampled.t.nwk","w"), schema="newick")
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Related Issues (20)
- SubsplitDAG: Export/Import Rimu-compatible JSON file
- macOS: Mmapping bug
- Extras reps_and_likelihoods: verify taxon ordering and variable number of input files
- NNI Engine: Optimize Branch Lengths
- NNI Engine: Top-Pruning HOT 5
- Top-Pruning, pt. 1: Choice Maps on SubsplitDAG HOT 5
- Extras reps_and_likelihoods: get newick strings
- Top-Pruning: PLVHandler Update
- Top-Pruning: ChoiceMap -- TreeMask Update and Build Trees HOT 3
- parsimony 1: perform Sankoff on trees HOT 2
- parsimony 2 Sankoff on DAG
- Top-Pruning: Top-Pruning Engine & Init on Tree HOT 2
- yet more iteration over unordered maps leading to inconsistent behavior
- TPEngine: Init DAG for Likelihood
- TPEngine: Init DAG for Parsimony
- TPEngine: Update after Add NNI
- TPEngine: Add Rescaling to Likelihood Computations
- TPEngine: Move PVs from Node-based to Edge-based HOT 2
- Interfaces for Evaluation Engines
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