You've run your tree, you like it, you've adjusted it just the way you want and now it's time to prepare it for publications. How do you do that? Let's go to one of our tree jobs. Click down here on to the jobs monitor. It reopens the page, writes the page and I'll take a tree that I like. I'll take this one. I've highlighted it. Remember when I click on anything, it populates the vertical green bar with possible downstream functions, and I want to view the tree. We've looked at niche 10 help, but what I'm going to show you is how to manipulate the tree in fig tree to get a better figure that you can use in a publication. This is a new AAC file. These are the instructions for building the tree that something like fig tree can interpret but this is with the genome IDs. As a biologist, I want to see the names, not the IDs. Let's click on detail files, this folder and here you'll see down at the bottom, trim the endosymbiont tree with genome names. That's the one I want. I click there and I'm going to click "Download," and I'll just say save the file. You know what? I'm going to click "Download" and open it for you too just so you can see what a newick file looks like. Believe it or not, these are the instructions for building a tree and this viewer can interpret that. You can go to fig tree and download the data here. It's a really nice little viewer, I like it a lot. I have it downloaded so I'm going to go back to Patrick, click on "Fig Tree." I'll make it bigger so that you can see it. This is what fig tree looks like when you open it on the computer. I will go on file and then I'll ask it to open and it gives me a dialog box with my computer and I'm going to go to downloads and click on date modified. Here's the one I want, the one with genome names. Click "Open." This is to show the bootstrap values and fig tree notices that we have something for that, it just wants us to name so that we can find it. I always call it support, you can call it A, it doesn't matter. This is originally how it opens and you don't see any bootstrap values, you see a lot of noise. Well, not noise but a tree that's hard to interpret. I go up into tree always and I click on "Midpoint Rooting" this is figuring out where the midpoint of the tree is. Then it's going to rearrange the tree and another thing that I like to do is going to tree and click on "Increasing Node Order." Now that's looking better. That's the way I like to see a tree. In any of these I can go in and for tip labels, I can click that and I can increase the size of the genome so that we can see those better. I can go into node labels, open that up, click on that and that's fig tree's interpretation. But if I, let me show you again under node ages, click down and support, those are my values. Those are the bootstrap values. You can increase the size of those if you wanted or decrease them. This is actually a nice tree that's got a nice number of genomes in it, and it looks pretty good. Let's see appearance, I can go in and I can increase the length of the lines if I wish. There's just a number of things that you can play with to make this as attractive as possible. I can go in and increase the scale bar down at the bottom and then increase the font size there so that you can see the substitutions. When I get everything the way I want and just let me point out how beautiful the support values are honestly, really nice. I think it looks really good when I get it to just the way I wanted. I can export it as a PDF, a scale vector graph, a PNG or JPEG and those are all things that I can generally journal some kinds like JPEG. You'll just have to figure out what exactly it is that the channel requires of you but there are all sorts of things you can do with it in here. Fig tree is a very nice little program to be able to manipulate your tree. In the last video, I'm going to show you how to find help on your tree and what describes the algorithms that we use and talk about citing all these statistics that you'll need to cite in your tree and how you credit us and the people who wrote the original parts of the tree pipeline that we combine in our pipeline. Thanks a lot. Bye. Patrick gives some beautiful trees, but one thing it doesn't get you is publication quality trees and that's why in the previous instructional video, I showed you how to use fig tree to get a better quality tree that you can submit with the publication. Because really that's all we want to do. We want to publish our data. In this assignment, you're going to be generating a figure yourself in fig tree. First I wants you to download fig tree, and you'll need now to go to GitHub to do it so you'll need to go to that URL that you see there on the screen. I want you to open fig tree on your computer and then within fig tree, open one of the newick files that you've downloaded. Now, here's what I'd suggest that you do, use one of the newick files with genome names, genome IDs when I'm trying to create a tree or I need to see the names to know who it is. Some people think in numbers on the name person, if you want to use numbers, go ahead but I would recommend the genome names. Once you have the tree open, I want you to turn on the support values so that you can see the bootstrap values there and feel confident in how well supported each of those branching patterns are. I want you to adjust the tree. Go ahead and play with the font size of both the genome names and the support values, midpoint, root the tree. That's an important thing to do especially with the bacterial genomes. You can arrange it whether you want it to be in increasing order or decreasing order, whatever, these are your trees, you want to make them as beautiful as you'd like them. Then I want you to export the PNG. From when I made the instructional video now you have to go to GitHub to download fig tree. I just did this today, I went to GitHub here and then I clicked on the dmg, when it downloaded, I clicked on that and I had to accept that I wasn't worried about it. I got it. Then you click on the figure for fig tree and you upload your newick file into it. You can do it. This is empowering you. Now you can not only run a tree pipeline but you can create the best figure that you can. Go ahead and practice now with this data, and then you'll have a lot of assurance that you can do it when it's your own data. Good luck.
