| Table of Contents |
|---|
1. Introduction
PhyloNet is a tool designed mainly for analyzing, reconstructing, and evaluating reticulate (or non-treelike) evolutionary relationships, generally known as phylogenetic networks. Various methods that we have developed make use of techniques and tools from the domain of phylogenetic trees, and hence the PhyloNet package includes several tools for phylogenetic tree analysis. PhyloNet is released under the GNU General Public License. For the full license, see the file GPL.txt included with this distribution.
...
| Input nexus file | Maximum number of reticulations | |
|---|---|---|
| InferNetwork_MPL_pl8_0_true.nex | 0 | |
| InferNetwork_MPL_pl8_1_true.nex | 1 | |
| InferNetwork_MPL_pl8_2_true.nex | 2 | |
| InferNetwork_MPL_pl8_3_true.nex | 3 | 4 |
| InferNetwork_MPL_pl8_4_true.nex | 4 |
Corresponding results: Fig 10 in the book chapter.
4.3.2 MPL Inference using gene tree topologies estimated by IQTREE
| Input nexus file | Maximum number of reticulations |
|---|---|
| InferNetwork_MPL_pl8_0_false.nex | 0 |
| InferNetwork_MPL_pl8_1_false.nex | 1 |
| InferNetwork_MPL_pl8_2_false.nex | 2 |
| InferNetwork_MPL_pl8_3_false.nex | 3 |
| InferNetwork_MPL_pl8_4_false.nex | 4 |
Corresponding results: Fig 10 in 11 in the book chapter.
4.3.
...
3 MPL Inference using bi-allelic marker data
| Input nexus file | Maximum Maximum number of reticulations |
|---|---|
| 0 | |
| 1 1 | |
| 2 | |
| 3 | |
| 4 |
Corresponding results: Fig 12 in the book chapter.
4.4 Bayesian Inference
4.4.1 MCMC_SEQ: Bayesian inference on the sequence alignment data
| Input nexus file | Maximum number of reticulations |
|---|---|
| 0 | |
| 1 | |
| 2 | |
| 3 | |
| 4 |
Corresponding results: Fig 13 in the book chapter.
4.4.2 MCMC_GT: Bayesian inference on gene tree topologies
| Input nexus file | Maximum number of reticulations |
|---|---|
| MCMC_GT_pl8_0_true.nex | 0 |
| 1 | |
| 2 | |
| 3 | |
| 4 |
4.4.3 MCMC_BiMarkers: Bayesian inference on the bi-allelic markers
| Input nexus file | Maximum number of reticulations | ||
|---|---|---|---|
| 0 | |||
| 1 | |||
| 2 | |||
| 3 | 4 | ||
| 4 |
...