Last time, we talked about the report that comes with any of the Codon Tree jobs. Now I'm going to walk you through some of the other files that come with any job. So let's find our job. We're going to it a different way. I'll go into WORKSPACES, click up here on this tab, and I'll click on My Jobs. This will open up the Job page for me and it's showing all the jobs that I've completed. Let me also note that if you have a lot of jobs and done a lot, you can see down here that right now I have over two thousand. I can click on this down arrow next to All Services and filter on just the jobs I want to see. Codon Trees. Let's look at the most recent job I did, which is this one, Endosymbionts May 2020, and it was 10 genes and I didn't do any duplications or deletions. We need to view the job, when I click on it, the vertical green bar allows me to report an issue with the job or to view it. Let's click on the View icon. Once again, at the top, this shows me where the job is placed in my workspace. It's in my home directory in a folder called Endosymbiont Trees. This is what I called it. Up at the top is the Job ID, how long it took to run. If I were to open this, it would show me all the parameters that were used in the job and the things I selected. Last time we talked about report HTML. But there are a bunch of different formats of the tree and the tree the way it's drawn in Patric, you can get the portable document format, which is the PDF of the same tree. You can get a PNG, which is a portable network graphics. You can get the SVG, which is the scalable vector graphics, that's a format that enables two-dimensional images to be viewed in XML pages on the web. We talked about the report. You can also get the nwk file itself. This is an important file. The nwk file is the minimal definition for a phylogenetic tree. If you want a tree that is publication quality, you're probably going to have to use a different program to visualize the tree and then get the picture of it and I'll show you why in a second. You'd need to download this file and upload it in either fig tree or the interactive tree of life. I use fig tree all the time and I'll show you how to do that in a later webinar. Another thing you can do, this is tree with genome ids as opposed to genome names. You can click on it and then look at the possible things you can do here, I can view that tree. Click here, and this will show me the tree in the Patric viewer right now and this is the same one we saw yesterday. We've got the Buchnera here, the [inaudible] , the endosymbionts of ants, [inaudible] , tsetse flies, and [inaudible] , which are the [inaudible]. One thing that you can do in Patric, by the way, when you have these kind of views is, remember when we were creating genome groups, when we were in the tree, clicking on these individual dots, I can click on a higher dot. It will select [inaudible] I could create a group from that tree, so that's pretty exciting. You can also see it as a phylogram or cladogram. That actually is a better way to see the support values for yourself. But if you wanted to publish this tree, which you wouldn't want to because it's only five genes and I'll show you how we can make this tree a lot better so it is publication quality and also with better support and also looking much more awesome, not due to our program, but due to the number of genes that you choose and things like that, you couldn't do it with these colors, so you would have to take it elsewhere as I said before. Let's go back to My Jobs page. We talked about these downloadable images of it. The report, that nwk file with the genome ids. Now when we looked at it, it had genome names because Patric renders it. But if you open this particular file in fig tree or the interactive tree of life, I told, you'll only see the genome ids. Many people want the names. How do I find the step with the names? Well look, here's another folder. Let's double-click on the detail files. Look what this opens, a whole bunch of other stuff. Genome analysis stats, those are included in the report that we talked about earlier. That if you wanted to download it and maybe put it in a publication, that's a downloadable format for it. Actually, this is anything that ends in text as a better downloadable format. The genes per genome.text, that's the same thing that you saw in the genomes report. It would show you the number of genes, the number of single copy genes, and the filtered single copy genes per genome that were used in the tree. The next file is the Nexus file format. This is something if you wanted to use Mr. Bay's, we use racks ML. This is a format that's used by those algorithms. Also, you can use a fig tree. We will use that to build a file. Partitionings is a commonly used method in bio-informatics and bio-genetics that aims to accommodate variation and substitution patterns along sides. This is actually a very boring little file, is just showing you when you're looking at the different stat sites in the genome were it started and where that position was. You can open it if you so desire. Sometimes people ask us for more information on the alignment. The alignment stats text show the statistics of the alignment and we could even view that so you can see what it looks like, anything that has a text button, we can view. This just shows shows me the PG fams, the gaps, the information about each of these across the top. I click the back button to go back. Phy is the file format, which is a plain text format that contains two sections. The header describing the dimensions of the alignment, followed by the multiple sequence alignment itself, if one wants to see that. raxmlCommand.sh is the actual shell script, shows the actual commands that were run. Aligned_pdf is the portable document format of the tree with the tips aligned. Aligned_png is the same thing except supportable networks graphic format and the scale vector format, SVG of the same thing. Here is the one I like the most. It's the tree with the genome names. That would be the one I would download and put into big tree because I like this one. The RAxML is the information about the version of the tree and everything else. I can't imagine any biologist ever even looking at this, but the computer scientists might really like to see that and it'll tell you the version of RAxML as well. Then the P3x_build_codon_tree log if one wanted to see it, it tells you exactly all the steps that went on. If there was a problem, this is something that we would open to look at to try to see what happened. Those are all the downloadable files in the future or the next little part of this series that we're going to do, I'm going to show you how to improve your tree. Remember when we looked at the report, we saw that if we eliminated some genomes, we'd get a better tree. I'm going to show you how to go into your group and get rid of genomes that you don't want to see. Also, I'm going to show you how you can look at using the protein family sorter, look at the protein families from the groups that you've created so that you can figure out first of all, how many genes you can use to build the tree, and also, if you should use the duplication or deletion function on particular group that you're looking at. Join me in that and thanks a lot for watching this one. In the webinar that goes with this assignment, I stepped you through all the downloadable files that come with any codon trees job. In this assignment, I want you to do it yourself. Go into the jobs and open each one and look at them. Here's a hint, if it doesn't open easily, use the text editor. Particularly important is to make sure you're comfortable downloading and opening the Newick file, which are the instructions for building the tree because we're going to have you play with that a little more later. Get going, get it done.
