SIMMAP | char coding

Character Coding

Character coding describes how SIMMAP interprets the user's description of the evolutionary model at a each site. For molecular data, in the context of SIMMAP, this describes how the data is partitioned into protein coding sites (i.e., codons). Thus, you are defining the translation coding region and reading frame. On the other hand, for morphological data coding describes whether a character's evolution is treated as "ordered" or "unordered". A more extensive description of each data type is presented below.

How to Modify Character Coding

There are two ways to initiate a change in character coding. By default SIMMAP assumes that morphological characters are treated as "unordered" while molecular characters are treated as nucleotides. The user can select the Set Character Coding... [4] item under the Data menu or if the Data View window is open the user can click on the Coding button. Either way a window will appear (shown to the right). If selected from the Data View window it will appear attached to the Data View.

Molecular Data

Molecular coding applies to the whole sequence in memory. To define a molecular (protein) coding region simply select the first character in the coding region (First coding site:), last character in the coding region (Last coding site:), and codon position of the first character (Codon position of first site:). You can enforce this coding be checking Show codons in Data View (Enforce coding) (This can be turned on and off using the Enforce Molecular Coding in the Data menu.).

Press the Apply button to accept the changes, or Cancel to exit the panel without making any changes. If you had collected results on codon character histories, you will be warned at this point that changing the coding region will remove these.If you wish to save the data before deleting it simply cancel this action and then go to the Codon Stats window, which can be displayed by selecting Show Codon Statistics... in the Statistics menu. Select the Save As button and proceed to save the results.

Morphological (Standard) Data

Morphological coding in the context discussed here refers to whether characters are considered to evolve in an unordered or ordered fashion. In the Morphological panel of the Character Coding window the current coding status of each character can be ascertained. To change a character(s) coding (un-ordered/ordered) simply select a character in either of the tables and use the arrow keys to move the character between categories (multiple characters can be moved by selecting multiple rows). Alternatively, the user can double-click the row with the cursor to move the character to the opposing table. Once you have finished making the desired modifications press the Apply button if satisfied or Cancel to revert to the previous coding.

A note on ordered evolution. SIMMAP uses a linear ordering scheme and does not allow character transformation trees to describe ordered evolution. An example of both ordering models for a 3-state character is shown below.

Page Last Updated: 6 August 2008


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