TreeSort
Real-time detection of influenza reassortment with a rigorous hypothesis testing framework. TreeSort on github.
PARNAS
A Python package for objectively sampling most representative taxa on a phylogeny and downsampling large trees while preserving diversity: PARNAS on github.
RF-Net 2
Java software for computation of Robinson-Foulds Reticulation Networks
- Software on the flu-crew github page: RF-Net 2
- Contact: Alexey Markin (amarkin (at) iastate (dot) edu)
PDC-Median
Joint Cophenetic and Path-Difference median tree software
- Software package (java): pdc-median.zip
- README: README-pdc-median.pdf
- Contact: Alexey Markin (amarkin (at) iastate (dot) edu)
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This software package combines the algorithms presented in the following manuscrips:
- Cophenetic Median Trees;
- Efficient Local Search for Euclidean Path-Difference Median Trees;
- Computing Manhattan Path-Difference Median Trees: a Practical Local Search Approach