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4.4.1 MCMC_SEQ: Bayesian inference on the sequence alignment data
To use MCMC_SEQ, you need to download an additional package beagle to calculate Felsenstein Likelihood. Please follow "Installing from source".
Add this package to your java library, and load this library before you run PhyloNet.
| Input NEXUS file | Maximum number of reticulations |
|---|---|
| 0 | |
| 1 | |
| 2 | |
| 3 | |
| 4 |
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4.4.3 MCMC_BiMarkers: Bayesian inference on the bi-allelic markers
Input NEXUS file: mcmc_bimarker.nexus
This method uses an additional package jeigen. You need to follow the instructions to install it, and add this package to your java library.
Input NEXUS file: mcmc_bimarker.nexus
This inference This inference ran out of 192 CPU hours.
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4.5.1 Tree-based Augmentation
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The -fs command in MP and MPL is to fix the start tree topology.
The following two examples are to infer a network using gene trees estimated by IQTREE and fixing the start species tree inferred by ASTRAL.
Input NEXUS file for MP: InferNetwork_MP_pl8_3_false_fs.nex
Input NEXUS file for MPL: InferNetwork_MPL_pl8_3_false_fs.nex
4.5.2 Divide-and-conquer
Data:
4.6 Analyzing Polyploids
This section corresponds to section 7 in the book chapter.
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