Phylogenetics - Back to Basics - Phylogenetic Networks

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# Phylogenetics - Back to Basics - Phylogenetic Networks

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  <a href="/training-material/hall-of-fame/mcharleston/" class="contributor-badge contributor-mcharleston"><img src="https://avatars.githubusercontent.com/mcharleston?s=36" alt="Michael Charleston avatar" width="36" class="avatar" />
    Michael Charleston</a>
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## Requirements

Before diving into this slide deck, we recommend you to have a look at:

- [Introduction to Galaxy Analyses](/training-material/topics/introduction)

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#About these slides
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<br>
The following phylogenetic networks of _Anolis_ species were generated in SplitsTree. They represent selected screenshots of networks explored as a live demo in the video associated with these slides.
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#Uncorrected P model
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Phylogenetic network of _Anolis_ species created in SplitsTree using the uncorrected P model. 
![Circular phylogenetic network with many branches splitting outwards from a central point to multiple Anolis species at the periphery. The network is oriented so that the species Diplolaemus darwinii and Phenacosaurus acutirostrus appear on the right hand side.](images/06-networks-uncorrectedP.png)
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#Exploring splits
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Click on the branches of the network to explore different splits. Here _A. ahli_ appears in two different splits highlighted in yellow.

.pull-left[ ![Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the bottom left of the image a split containing A. ahli, A. equestris2 and several other species is highlighted in yellow](images/06-networks-explore_split_1.png) ]

.pull-right[ ![Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the top left of the image a split containing A. ahli, A. bimaculatus and several other species is highlighted in yellow](images/06-networks-explore_split_2.png) ]

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#Let's follow a split
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This is the network made using the uncorrected p model. We will follow the split containing _A. lineatopus_ and _A. limifrons_ through different models.

![Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the bottom left of the image a split containing A. lineatopus and A. limifrons is highlighted in yellow](images/06-networks-unP-follow-split.png)

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#Jukes Cantor Model
<br>
These networks were created using the Jukes Cantor model. Note that the species _A. limifrons_ appears in two alternate splits.

.pull-left[ ![Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the bottom left of the image a split containing A. limifrons and A. humilis is highlighted in yellow](images/06-networks-JC_split1.png) ]

.pull-right[ ![Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the bottom left of the image a split containing A. lineatopus and A. limifrons is highlighted in yellow](images/06-networks-JC_split2.png) ]
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#HKY85 Model 
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This network was created with the HKY85 model. Note that _A. limfrons_ is paired with _A. humilis_ in this split.

![Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the top left of the image a split containing A. humilis and A. limifrons is highlighted in yellow](images/06-networks-HKY85_split.png)
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#Bootstrapped network
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![Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. Each branch is annotated with a value between 0-100](images/06-networks-bootstrap.jpg)
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#Bootstrapped network - a closer look
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Let's explore our two splits again

.pull-left[ ![Close up screen shot of a section of a circular phylogenetic network with multiple branches splitting out from a central point. The split containing A. humilis and A. limifrons is highlighted in yellow and is annotated with the value 99.99](images/06-networks-bootstrap-split1.jpg) ]

.pull-right[ ![Close up screen shot of a section of a circular phylogenetic network with multiple branches splitting out from a central point. The split containing A. lineatopus and A. limifrons is highlighted in yellow and is annotated with the value 38.3](images/06-networks-bootstrap-split2.jpg) ]
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#Bootstrapped network - a closer look
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This the centre of our bootstrapped network. Note that the values are smaller.
![Close up screen shot of a section of a circular phylogenetic network with multiple branches splitting out from a central point. The splits form a star like shape and are annotated with numbers](images/06-networks-bootstrap-centre.jpg)

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# Thank you!

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
		<td>
			
  <a href="/training-material/hall-of-fame/mcharleston/" class="contributor-badge contributor-mcharleston"><img src="https://avatars.githubusercontent.com/mcharleston?s=36" alt="Michael Charleston avatar" width="36" class="avatar" />
    Michael Charleston</a>
  
		</td>
	</tr>

<tr class="reviewers">
		<td><abbr title="These people reviewed this material for accuracy and correctness">Reviewers</abbr></td>
		<td>
			
  <a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena">
    <img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/burkemlou/" class="contributor-badge contributor-burkemlou">
    <img src="https://avatars.githubusercontent.com/burkemlou?s=36" alt="Melissa Burke avatar" width="36" class="avatar" />
  </a>
  
  <a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-shiltemann">
    <img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" />
  </a>
  </td>
	</tr>

</table>

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Tutorial Content is licensed under <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.<br/>