This is a Snakemake workflow that calculates maximum-likelihood gene trees with IQ-TREE and 100 bootstrap replicates for each tree. Then, consensus trees are produced and combined to infer a species tree following the multispecies coalescent model with ASTRAL. Imported from my GitLab.
Bayesian estimation of conditional clade distributions etc.
R package to test the multi-species coalescent model using trees estimated with starBEAST2 and to estimate false-positive error rates based on samples from the posterior predictive distributions
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