Software

• PhyloNetworks package (in Julia), for the manipulation and inference of phylogenetic networks and admixture graphs, including the pseudolikelihood method SNaQ.
  
  Companion packages:
  
  PhyloPlots to plot phylogenetic networks
  QuartetNetworkGoodnessFit to test the adequacy of a phylogenetic network
  PhyloCoalSimulations to simulate gene trees under the network multispecies coalescent
  PhyloGaussianBeliefProp for continuous trait evolution using belief propagation techniques
  
• TICR pipeline, for highly parallelized concordance analyses and population tree reconstruction and testing.
• iBPP: Bayesian species delimitation using both multiple genes and multiple traits. This tarball includes the source code, examples, and documentation for version 2.1.2.
• Detection of whole genome duplications from multiple gene families.
• phylolm: R package for fitting phylogenetic regression models (linear, logistic and Poisson), using a fast algorithm linear in the number of taxa. This algorithm replaces matrix inversion and enables the analysis of trees with thousands of tips. Available on CRAN or pull from GitHub for the most recent version.
• ℓ1ou: R package to detect shifts in trait evolution processes. Requires phylolm.
• Minimum Description Length for the detection of phylogenetics breakpoints: tarball or as part of the TICR pipeline on GitHub. For the method, refer to this GBE paper.
• BUCKy: for Bayesian Concordance Analysis. Molecular data from multiple loci are combined to estimate the dominant history of sampled individuals, and how much of the genome supports each relationship.
• Test for Covarion evolution.
• seq-gen-cov: a modification of seq-gen. C program that simulates nucleotide sequences under a variety of models, including the covarion models (executable compiled under linux). Source files: .tar.gz or here along with a Makefile, in case you wish to compile it on your machine or want to adapt the code to your needs.