# PhyloNetworks.jl
**Repository Path**: yen233/PhyloNetworks.jl
## Basic Information
- **Project Name**: PhyloNetworks.jl
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No
## Statistics
- **Stars**: 0
- **Forks**: 0
- **Created**: 2020-11-20
- **Last Updated**: 2024-05-30
## Categories & Tags
**Categories**: Uncategorized
**Tags**: None
## README
# PhyloNetworks: analysis for phylogenetic networks 
[](https://travis-ci.org/crsl4/PhyloNetworks.jl)
[](https://crsl4.github.io/PhyloNetworks.jl/stable)
[](https://crsl4.github.io/PhyloNetworks.jl/dev)
[](https://codecov.io/gh/crsl4/PhyloNetworks.jl)
[](https://coveralls.io/github/crsl4/PhyloNetworks?branch=master)
## Overview
PhyloNetworks is a [Julia](http://julialang.org) package with utilities to:
- read / write phylogenetic trees and networks,
in (extended) Newick format.
Networks are considered explicit: nodes represent ancestral species.
They can be rooted or unrooted.
- manipulate networks: re-root, prune taxa, remove hybrid edges,
extract the major tree from a network, extract displayed networks / trees
- compare networks / trees with dissimilarity measures
(Robinson-Foulds distance on trees)
- summarize samples of bootstrap networks (or trees)
with edge and node support
- estimate species networks from multilocus data (see below)
- phylogenetic comparative methods for continuous trait evolution
on species networks / trees
- plot networks (and trees), via the companion package
[PhyloPlots](https://github.com/cecileane/PhyloPlots.jl)
To get help, check
- the [latest documentation](https://crsl4.github.io/PhyloNetworks.jl/dev)
- the [wiki](https://github.com/crsl4/PhyloNetworks.jl/wiki) for a step-by-step tutorial
(July 2018) with background on networks
- the [google group](https://groups.google.com/forum/#!forum/phylonetworks-users)
for common questions. Join the group to post/email your questions,
or to receive information on new versions, bugs fixed, etc.
If you use the package, please cite
- Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017).
PhyloNetworks: a package for phylogenetic networks.
[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)
34(12):3292–3298.
[doi:10.1093/molbev/msx235](https://doi.org/10.1093/molbev/msx235)
## Maximum pseudolikelihood estimation of species network: SNaQ 
SNaQ implements the statistical inference method in Solís-Lemus and Ané
[(2016)](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896).
The procedure involves a
numerical optimization of branch lengths and inheritance probabilities
and a heuristic search in the space of phylogenetic
networks.
If you use SNaQ, please cite
- Claudia Solís-Lemus and Cécile Ané (2016).
Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting.
[PLoS Genet](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896)
12(3):e1005896.
[doi:10.1371/journal.pgen.1005896](https://doi.org/10.1371/journal.pgen.1005896)
## Phylogenetic comparative methods for trait evolution
For continuous traits, study based on the Brownian motion process,
with or without transgressive evolution after reticulations:
- Bastide, Solís-Lemus, Kriebel, Sparks, Ané (2018).
Phylogenetic Comparative Methods for Phylogenetic Networks with Reticulations.
Systematic Biology, 67(5):800–820.
[doi:10.1093/sysbio/syy033](https://doi.org/10.1093/sysbio/syy033).
SI on [dryad](http://dx.doi.org/10.5061/dryad.nt2g6)
including a [tutorial for trait evolution](https://datadryad.org/bitstream/handle/10255/dryad.177752/xiphophorus_PCM_analysis.html?sequence=1)
and a [tutorial for network calibration](https://datadryad.org/bitstream/handle/10255/dryad.177754/xiphophorus_networks_calibration.html?sequence=1).