Now that we have a list of characters and know how to create our OTUs we are set to create matrices. The first thing to understand, however, is that the codings are not stored in the actual matrices. If you change how a certain OTU is coded for a certain character it will change everywhere where this combination of OTU and character occurs. This also means that if you code subsets of either characters or taxa and then combine them into a larger matrix, all codings will show there too. Since large matrices can be problematic both when it comes to layout and computer resources, smaller subsets are recommended when carrying out the actual coding.
When choosing the Matrices tab you get a listing of all currently available matrices (Fig. 7). If you want to start from scratch and create a new matrix you simply click New mx in the top left corner. All you have to do at the first step is give it a name. Next, you are presented with some basic information and a few options (Fig. 17). Basically, in the menu to the left, you click the OTUs link to add (or code by) OTUs and characters to add (or code by) characters. If you have created groups of OTUs and/or characters you can add those whole groups here also. When you add something, it shows up in a list below the boxes used for adding (Figs 18 & 19). There are links to change the position of the OTUs if you like. Important: once you are done adding characters you need to click on Sort characters as seen in figure 19. No need to do anything more, but if you like you can rearrange the order of the characters also.