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Update Dendroscope Link in Orthofinder Tutorial #1

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4 changes: 2 additions & 2 deletions _posts/2019-09-20-exploring-orthofinders-results.md
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Expand Up @@ -37,7 +37,7 @@ That's pretty good, in general it's nice to see at least 80% of your genes assig
Once you've opened this file you'll see that the vertebrates all have over 90% of their genes assigned to orthogroups whereas *Drosophila* has about 76% of its genes assigned. This is probably due to species sampling. The four vertebrate species are all relatively closely related whereas the species sampling around both *Drosophila* and *C. elegans* was poor. To improve this we would need to include some species that break up the long branches in the species tree separating these species from all the others.

## Species Tree
Let's look at the species tree next. [Dendroscope](http://dendroscope.org/) is a tree viewer you can download and run locally and is the best option if you're going to look at more than a few trees. Alternatively, there are also a number of options you can run from you're web browser, e.g. the [ETE Toolkit tree viewer](http://etetoolkit.org/treeview/). Using one of these, open the file **Species_Tree/SpeciesTree_rooted.txt**. As this file has bootstrap values Dendroscope will need you to select the option "Interpret as edge labels" to view them correctly. The species tree looks like this:
Let's look at the species tree next. [Dendroscope](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/dendroscope/) is a tree viewer you can download and run locally and is the best option if you're going to look at more than a few trees. Alternatively, there are also a number of options you can run from you're web browser, e.g. the [ETE Toolkit tree viewer](http://etetoolkit.org/treeview/). Using one of these, open the file **Species_Tree/SpeciesTree_rooted.txt**. As this file has bootstrap values Dendroscope will need you to select the option "Interpret as edge labels" to view them correctly. The species tree looks like this:

<img src="{{ site.github.url }}/assets/img/SpeciesTree_rooted.png">

Expand Down Expand Up @@ -99,4 +99,4 @@ For each orthogroup there is a FASTA file in **Orthogroup_Sequences/** which con
## Other Results Files
We'll look at some more of the results files in the next tutorial. You can also see a complete listing on the GitHub page here: [https://github.com/davidemms/OrthoFinder#what-orthofinder-provides](https://github.com/davidemms/OrthoFinder#what-orthofinder-provides).

The GitHub page also contains a discussion of [orthologues, paralogues and orthogroups](https://github.com/davidemms/OrthoFinder/#orthogroups-orthologs--paralogs).
The GitHub page also contains a discussion of [orthologues, paralogues and orthogroups](https://github.com/davidemms/OrthoFinder/#orthogroups-orthologs--paralogs).