Software

Open-Source Projects

PhyNEST.jl

Phylogenetic Network Estimation using Site Patterns (Julia)
PhyNEST.jl is a Julia package for inferring phylogenetic networks from sequence alignments using site pattern-based methods. It enables robust estimation of complex reticulate evolutionary histories under the multispecies network coalescent model.

• Written in pure Julia for speed and flexibility
• Accepts data in Nexus and Phylip formats
• Supports hybridization and incomplete lineage sorting
• Includes utilities for visualizing and analyzing networks
• Integrates with PhyloNetworks.jl

Status: Actively developed | License: MIT
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SymbolicQuartetNetworkCoal.jl

Symbolic Computation of Expected Quartet Concordance Factors
SymbolicQuartetNetworkCoal.jl is a Julia package for symbolically computing expected concordance factors under the network multispecies coalescent model. It supports exact symbolic derivations and is ideal for theoretical work and benchmarking.

• Derives closed-form expressions for concordance factors
• Supports both tree and reticulate topologies
• Symbolic manipulation of coalescent probabilities
• Built using Julia’s symbolic computation libraries

Status: Research-ready | License: MIT
🔗 View on GitHub

If you use these tools in your research, please cite the relevant software or publications (see Research). Contributions and feedback are welcome!