iTOL

This week was productive in a way, and slow in another. The main progress I made this week was researching different online phylogenetic tree displays in order to hopefully find one that I could use for my final result. The requirements for that included it being compatible with HTML so that ideally I could put it on a separate page on this site, and it having the interactive features I want such as a “hover-over” box of information including embedded YouTube videos, and a list of characteristics. I found one! So of a list of products to check, six of them in total, two were eliminated immediately, two were borderline and I wasn’t sure if they would be a good format fit for this project, another one was a downloadable software that looked promising (my current backup plan), and the last one seems extremely promising and versatile. The program is an online interface called iTOL (interactive tree of life) that allows users to upload and manage their phylogenetic trees on the site, and the features I saw covered all of the specifications I hope to include in my final project. This discovery changes how I’m going to be continuing with this project immensely, in terms of application at least. The main focus and results of the project are remaining the same.

So in order to use iTOL to work with my tree I need to take my data and put it into an appropriate format that iTOL can recognize and compile for me. My options are Newick, Nexus, and PhyloXML. I’ve vaguely heard of all of these, but I have actual experience with none of them. iTOL provides a bit of aid in how to use the three, and I’m sure I can find plenty of tutorials on each if need be. The primary difference now is that instead of working on drawing the tree myself, which would be extremely inefficient, I will be spending more time converting my data into one of the three compatible formats.

In addition to the tree file itself, iTOL provides many dataset templates that I can then apply to the tree. These vary in complexity. The most basic one is simply a text label dataset that matches each leaf with a label, which I will definitely include. There are four others that I’m considering as well: branch symbols, multi-value bar charts or shape plots, and connections. Branch symbols would place shapes as specific junctions in the tree, which could be a good way to show where characteristics appeared, if it doesn’t make the tree too cluttered. Connections would almost certainly make the tree cluttered, but if it’s a feature that I could toggle on and off then in might be a nice addition. It would show any possible parallel relationships similar to the biological concept of horizontal gene transfer. Both shape plots and multi-value bar charts would show the characteristics of each leaf at the leaf itself, which would definitely be useful. At the moment I’m leaning towards the multi-value bar charts because I think it provides room for more characteristics.

For next week I’ll have hopefully started some of the data conversion!
Once I make this first prototype tree I’ll go back and work on splitting up the bunches.

Genre of the week: Beat music/Merseybeat

Beat rock is credited with being the first genre to define the “standard” rock band line-up as a lead and rhythm guitar, a bass guitar, and drums. The subgenre is primarily tied to Britain, specifically locations such as Liverpool and Manchester, and is mostly responsible for the British Invasion.

One of my favorite Beatles songs:

and another good example:

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