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1 | | -# PhyloNetworks: analysis for phylogenetic networks <img src="docs/src/logo_text.png" align=right> |
2 | | - |
3 | 1 | [](https://juliaphylo.github.io/PhyloNetworks.jl/stable) |
4 | 2 | [](https://juliaphylo.github.io/PhyloNetworks.jl/dev) |
5 | 3 | [](https://github.com/juliaphylo/PhyloNetworks.jl/actions/workflows/ci.yml) |
|
8 | 6 | [](https://github.com/SciML/ColPrac) |
9 | 7 | [](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/report.html) |
10 | 8 |
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| 9 | +<div align="right"> |
| 10 | + |
| 11 | +  |
| 12 | +  |
| 13 | + |
| 14 | +</div> |
| 15 | + |
11 | 16 | ## Overview |
12 | 17 |
|
13 | | -PhyloNetworks is a [Julia](http://julialang.org) package with utilities to: |
14 | | -- read / write phylogenetic trees and networks, |
15 | | - in (extended) Newick format. |
16 | | - Networks are considered explicit: nodes represent ancestral species. |
17 | | - They can be rooted or unrooted. |
| 18 | +PhyloNetworks is a [Julia](http://julialang.org) package with utilities to |
| 19 | +to handle phylogenetic trees and networks. |
| 20 | +It serves as a core package that other packages can depend on, such as |
| 21 | +[PhyloPlots](https://github.com/JuliaPhylo/PhyloPlots.jl) |
| 22 | +to visualize phylogenies, |
| 23 | +[SNaQ](https://github.com/JuliaPhylo/PhyloPlots.jl) |
| 24 | +to infer phylogenies from genetic data, |
| 25 | +[PhyloTraits](https://github.com/JuliaPhylo/PhyloTraits.jl) |
| 26 | +to analyze the evolution of traits along phylogenies. |
| 27 | + |
| 28 | +Phylogenetic networks represent the evolutionary relationships between a set |
| 29 | +of organisms, e.g. populations, species, languages, cultures etc. |
| 30 | +They are also called *admixture graphs* when their leaves are populations |
| 31 | +of the same or closely related species. |
| 32 | +They are *explicit* graph representations, in which nodes represent |
| 33 | +ancestral populations / species, and edge lengths represent evolutionary time. |
| 34 | + |
| 35 | +Utilities in this core package include: |
| 36 | +- read / write phylogenies in (extended) Newick format |
18 | 37 | - manipulate networks: re-root, prune taxa, remove hybrid edges, |
| 38 | + transform a network with a semidirected nearest-neighbor interchange (sNNI), |
19 | 39 | extract the major tree from a network, extract displayed networks / trees |
20 | | -- compare networks / trees with dissimilarity measures |
21 | | - (Robinson-Foulds distance on trees) |
22 | | -- summarize samples of bootstrap networks (or trees) |
23 | | - with edge and node support |
24 | | -- estimate species networks from multilocus data: SNaQ |
25 | | -- phylogenetic comparative methods for continuous trait evolution |
26 | | - on species networks / trees |
27 | | -- plot networks (and trees), via the companion package |
28 | | - [PhyloPlots](https://github.com/juliaphylo/PhyloPlots.jl) |
| 40 | +- compare networks with dissimilarity measures |
| 41 | + (e.g. the Robinson-Foulds distance on trees) |
| 42 | +- summarize samples of networks with support for local features |
| 43 | + (edges and clades of hybrid origin or sister to a hybrid clade) |
| 44 | +- fit edges lengths from average pairwise distances between leaves, |
| 45 | + using least-squares |
| 46 | +- network traversal routines |
29 | 47 |
|
30 | 48 | To get help, check |
31 | 49 |
|
32 | 50 | - the [latest documentation](https://juliaphylo.github.io/PhyloNetworks.jl/dev) |
33 | | -- the [wiki](https://github.com/juliaphylo/PhyloNetworks.jl/wiki) for a step-by-step tutorial |
34 | | - with background on networks (last revised 2022) |
| 51 | +- the [wiki](https://github.com/juliaphylo/PhyloNetworks.jl/wiki) for a |
| 52 | + step-by-step tutorial with background on networks (last revised 2022) |
35 | 53 | - [tutorial](https://cecileane.github.io/networkPCM-workshop/) for |
36 | 54 | comparative methods, including network calibration (2023 workshop) |
37 | 55 | - the [google group](https://groups.google.com/forum/#!forum/phylonetworks-users) |
38 | 56 | for common questions. Join the group to post/email your questions, |
39 | 57 | or to receive information on new versions, bugs fixed, etc. |
40 | 58 |
|
41 | | -If you use the package, please cite ([bibtex format here](CITATION.bib)) |
| 59 | +If you use the package, please cite ([bibtex format here](CITATION.bib)). |
| 60 | +For the PhyloNetworks package in particular, please cite: |
42 | 61 |
|
43 | 62 | - Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017). |
44 | 63 | PhyloNetworks: a package for phylogenetic networks. |
45 | 64 | [Molecular Biology and Evolution](https://academic.oup.com/mbe/article/doi/10.1093/molbev/msx235/4103410/PhyloNetworks-a-package-for-phylogenetic-networks?guestAccessKey=230afceb-df28-4160-832d-aa7c73f86369) |
46 | 65 | 34(12):3292–3298. |
47 | 66 | [doi:10.1093/molbev/msx235](https://doi.org/10.1093/molbev/msx235) |
48 | 67 |
|
49 | | -## Maximum pseudolikelihood estimation of species network: SNaQ <img src="docs/src/snaq.png" align=right title="SNaQ logo" width=262.5 height=111> |
50 | | -<!--  |
51 | | -original size: 525px × 222px--> |
52 | | - |
53 | | -SNaQ implements the statistical inference method in Solís-Lemus and Ané |
54 | | -[(2016)](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896). |
55 | | -The procedure involves a |
56 | | -numerical optimization of branch lengths and inheritance probabilities |
57 | | -and a heuristic search in the space of phylogenetic |
58 | | -networks. |
59 | | - |
60 | | -If you use SNaQ, please cite |
61 | | - |
62 | | -- Claudia Solís-Lemus and Cécile Ané (2016). |
63 | | - Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting. |
64 | | - [PLoS Genet](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896) |
65 | | - 12(3):e1005896. |
66 | | - [doi:10.1371/journal.pgen.1005896](https://doi.org/10.1371/journal.pgen.1005896) |
67 | | - |
68 | | -## Phylogenetic comparative methods for trait evolution |
69 | | - |
70 | | -For continuous traits, study based on the Brownian motion process, |
71 | | -with or without transgressive evolution after reticulations: |
72 | | - |
73 | | -- Bastide, Solís-Lemus, Kriebel, Sparks, Ané (2018). |
74 | | - Phylogenetic Comparative Methods for Phylogenetic Networks with Reticulations. |
75 | | - Systematic Biology, 67(5):800–820. |
76 | | - [doi:10.1093/sysbio/syy033](https://doi.org/10.1093/sysbio/syy033). |
77 | | - SI on [dryad](http://dx.doi.org/10.5061/dryad.nt2g6) |
78 | | - including a tutorial for trait evolution |
79 | | - and a tutorial for network calibration. |
80 | | - |
81 | | -Continuous traits, accounting for within-species variation: |
82 | | - |
83 | | -- Benjamin Teo, Jeffrey P. Rose, Paul Bastide & Cécile Ané (2022). |
84 | | - Accounting for intraspecific variation in continuous trait evolution |
85 | | - on a reticulate phylogeny. |
86 | | - [bioRxiv](https://doi.org/10.1101/2022.05.12.490814) |
87 | | - |
88 | | -For a discrete trait (influence of gene flow on the trait, |
89 | | -ancestral state reconstruction, rates): |
90 | | - |
91 | | -- Karimi, Grover, Gallagher, Wendel, Ané & Baum (2020). Reticulate evolution |
92 | | - helps explain apparent homoplasy in floral biology and pollination in baobabs |
93 | | - (*Adansonia*; Bombacoideae; Malvaceae). |
94 | | - Systematic Biology, |
95 | | - 69(3):462-478. doi: [10.1093/sysbio/syz073](https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz073/5613901?guestAccessKey=a32e7dd3-27fd-4a13-b171-7ff5d6da0e01). |
| 68 | +> [!NOTE] |
| 69 | +> Version 0.17 of PhyloNetworks is a major change from version v0.16.4. Many |
| 70 | +> functionalities were moved to other packages (e.g. SNaQ.jl and PhyloTraits.jl), |
| 71 | +> the names of many methods were changed, and various internal functions |
| 72 | +> were improved with breaking changes (e.g. traversal routines). |
| 73 | +> PhyloNetworks v0.17 should serve as a better "core", used by other packages |
| 74 | +> with more specialized functionalities. |
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