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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 treesnetworks, and hence the PhyloNet package includes several tools for phylogenetic tree analysisnetwork analysis. PhyloNet is released under the GNU General Public License. For the full license, see the file GPL.txt included with this distribution.
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In order to run the PhyloNet toolkit, you must have Java 1.78.0 or later installed on your system. All references to the java command assume that Java 1.7 is being used.
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java -jar $PHYLONET_DIRECTORY/PhyloNet_X.Y.Z.jar script.nex |
Where $PHYLONET$PHYLONET_PATH DIRECTORY is the directory of jar file PhyloNet_X.Y.Z.jar, and script.nex is the NEXUS file containing the commands to be executed.
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| Input NEXUS file | Maximum number of reticulations |
|---|---|
| mle_bi_0pseudo.nexus | 0 |
| mle_bi_1pseudo.nexus | 1 |
| mle_bi_2pseudo.nexus | 2 |
| mle_bi_3pseudo.nexus | 3 |
| mle_bi_4pseudo.nexus | 4 |
Corresponding results: Fig 12 in the book chapter.
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4.4.1 MCMC_SEQ: Bayesian inference on the sequence alignment data
| Input NEXUS file | Maximum number of reticulations |
|---|---|
| 0 | |
| 1 | |
| 2 | |
| 3 | |
| 4 |
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.
One input example: mcmc_seq.nex
All input NEXUS files: download
Corresponding results: Fig 13 in the book chapter.
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4.4.3 MCMC_BiMarkers: Bayesian inference on the bi-allelic markers
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 ran out of 192 CPU hours.
4.5 Analyzing Larger Data Sets
This section corresponds to section 5 in the book chapter.
4.5.1 Tree-based Augmentation
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
The data set contains the MCMC_SEQ outputs of 680 trinets. You need to download the data and change the path ".../DivideAndConquer/" in netmerger.nex.
Data: https://drive.google.com/file/d/1mJfqD0bQOOoBFZTlaQklHLqvJX5QPlVg/view?usp=sharing
Input NEXUS file: netmerger.nex
4.6 Analyzing Polyploids
This section corresponds to section 7 in the book chapter.
4.6.1 MDC Inference with unknown hybrid species
| Input NEXUS file | Maximum number of reticulations |
|---|---|
| InferNetwork_MP_0.nex | 0 |
| 1 | |
| InferNetwork_MP_1.nex | 1 |
| InferNetwork_MP_2.nex | 2 |
| InferNetwork_MP_3.nex | 3 |
| 4 |
Corresponding results: Fig 17 in the book chapter.
4.6.2 MDC Inference with known hybrid species
| Input NEXUS file | Maximum number of reticulations | Specified hybrid species |
|---|---|---|
| InferNetwork_MP_1.nex | 1 | LPS168 |
| InferNetwork_MP_2.nex | 2 | LPS168 |
| InferNetwork_MP_2_2.nex | 2 | LPS168, LPS189 |
| InferNetwork_MP_3.nex | 3 | LPS168 |
| InferNetwork_MP_3_2.nex | 3 | LPS168, LPS189 |
Corresponding results: Fig 18 in the book chapterThis inference ran out of 192 CPU hours.
5. Visualizing a Phylogenetic Network
Phylogenetic network in Rich Newick string can be visualized in Dendroscope or icytree. The former needs downloading, and the latter is online. However, neither can Dendroscope cannot recognize inheritance probabilities (branch lengths are fine), and icytree sometimes can and sometimes cannot. You have need to remove those probabilities manually from the Rich Newick string, or use option "-di" so that PhyloNet returns the network that Dendroscope takes directly. For example, the following network is what PhyloNet returns when the input NEXUS file InferNetwork_MPML_pl8_1_true.nex is used:
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((F:12.842,((L:5.576504712905155,((Skud,(Sbay)#H1::O:1.2260000000000002,P:1.2260000000000002)I6:0.36082474226804123),((Spar,Scer),Smik)),#H1:8559999999999997,K:2.082)I2:3.4945047129051554)I0:0.08027116443257487)I8#H1:7.18522412266227::0.63917525773195874334172270375128),Scas),Sklu),Calb);I1:19.128,(I8#H1:1.81722412266227::0.5665827729624873,C:7.474)I4:24.496000000000002)I7; |
After removing "::" and the number after it, we have the network below, which can be visualized in both tools.In order to visualize this phylogenetic network in Dendroscope, please remove the inheritance probabilities like follows, and Dendroscope will be able to read it. Or you can use option "-di".
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((F:12.842,((((Skud,(Sbay)#H1),((Spar,Scer),Smik)),#H1),Scas),Sklu),Calb);L:5.576504712905155,((O:1.2260000000000002,P:1.2260000000000002)I6:0.8559999999999997,K:2.082)I2:3.4945047129051554)I0:0.08027116443257487)I8#H1:7.18522412266227)I1:19.128,(I8#H1:1.81722412266227,C:7.474)I4:24.496000000000002)I7; |
6. References
- . PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships. BMC Bioinformatics, 9:322, 2008
- C. Than and L. Nakhleh. Species tree inference by minimizing deep coalescences. PLoS Computational Biology, 5(9):e1000501, 2009.
- Y. Yu, T. Warnow, and L. Nakhleh. Algorithms for MDC-based multi-locus phylogeny inference. Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), LNBI 6577, 531-545, 2011.
- Y. Yu, T. Warnow, and L. Nakhleh. Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles. Journal of Computational Biology, 18(11):1-18, 2011.
- Y. Yu, J.H. Degnan, and L. Nakhleh. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics, 8(4):e1002660, 2012.
- Y. Yu, R.M. Barnett, and L. Nakhleh. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology, vol. 62, no. 5, pp. 738-751, 2013.
- Y. Yu and L. Nakhleh. Fast algorithms for reconciliation under hybridization and incomplete lineage sorting. BMC Bioinformatics, vol. 14, no. Suppl 15, p. S6, 2013.
- Y. Yu, J. Dong, K. Liu, and L. Nakhleh, “Probabilistic inference of reticulate evolutionary histories,” Proceedings of the National Academy of Sciences, vol. 111, no. 46, pp. 16448-16453, 2014.
- , “A Maximum Pseudo-likelihood Approach for Phylogenetic Networks”, BMC Genomics, vol. 16, no. Suppl 10, p. S10, 2015.
- , “Reticulate Evolutionary History and Extensive Introgression in Mosquito Species Revealed by Phylogenetic Network Analysis”, Molecular Ecology, vol. 25, pp. 2361-2372, 2016.
- , “Bayesian inference of species phylogenies under the multispecies network coalescent”, PLoS Genetics, vol. 12, no. 5, p. e1006006, 2016.
- D.Wen and L. Nakhleh. Co-estimating reticulate phylogenies and gene trees on sequences from multiple independent loci. Systematic Biology 67.3 (2017): 439-457.
- Z. Cao, X. Liu, HA. Ogilvie, Z. Yan, and L. Nakhleh. Practical aspects of phylogenetic network analysis using phylonet. bioRxiv (2019): 746362.
- Z. Cao, J. Zhu, and L. Nakhleh. Empirical Performance of Tree-Based Inference of Phylogenetic Networks. WABI 2019.