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- GitHub - veg/hyphy-analyses: HyPhy standalone analyses
- Labeling phylogenetic tree programatically · Issue #40 · veg/hyphy-analyses · GitHub
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- Problems with different output results · Issue #1551 · veg/hyphy · GitHub
- RELAX problem with tree · Issue #1034 · veg/hyphy · GitHub
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- Interpret the results of the MEME model · Issue #1639 · veg/hyphy · GitHub