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Where script.nex is the NEXUS file containing the commands to be executed.
4. Illustrating Illustrating the Various Inference Methods in PhyloNet
Here we provide all the input nexus files in section 4 of the book chapter.
4.1
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Minimize deep coalescent Inference
This section corresponds to section 4.1 of the book chapter.
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4.4.2 MCMC_GT: Bayesian inference on gene tree topologies
4.4.2.1 MCMC_GT sampling using true gene tree topologies
| Input nexus file | Maximum number of reticulations |
|---|---|
| MCMC_GT_pl8_0_true.nex | 0 |
| MCMC_GT_pl8_1_true.nex | 1 |
| MCMC_GT_pl8_2_true.nex | 2 |
| MCMC_GT_pl8_3_true.nex | 3 |
| MCMC_GT_pl8_4_true.nex | 4 |
4.4.2.2 MCMC_GT sampling using gene tree topologies estimated by IQTREE
| Input nexus file | Maximum number of reticulations |
|---|---|
| MCMC_GT_pl8_0_false.nex | 0 |
| MCMC_GT_pl8_1_false.nex | 1 |
| MCMC_GT_pl8_2_false.nex | 2 |
| MCMC_GT_pl8_3_false.nex | 3 |
| MCMC_GT_pl8_4_false.nex | 4 |
4.4.3 MCMC_BiMarkers: Bayesian inference on the bi-allelic markers
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