Program interface for FastMorphologyGFC
FastMorphologyGFC has been design to have a very simple interface with the user, making decision taking on behalf of the analyzer as simple as possible under the Paup interface.
1.After opening (unzipping and opening FastMorphologyGFC.exe) press on the Load Input button and choose the input matrix from the menu.
2.Press "Process", on the window the Nexus file will appear and you can edit the file directly before saving. If you need to place notes remember to do it in brackets, so that Paup will not read the contents.
3.Save Output or Quit by pressing the corresponding buttons. When saving it is useful to end the name of the file as *.txt or *.nex. Doing this will make the file readable for programs using nexus or text files. For the particular example we have named a file PokemonPaup.txt, this is a nexus file created with FastMorphologyGFC.
4.Files can be saved only once for each run.
The |FastMorphologyGFC-Nexus-file| in Paup
Since all characters have been transformed into subcharacters for both cumulative and noncumulative frequencies it is necessary to choose which sets of characters are appropriate for analysis depending on the original nature of the characters. We recommend that before selecting "characters" to be used in the analysis you Exclude all, Data menu, "Include-Exclude Characters..."
The Pokemon data matrix exemplifies the use of 4 types of characters:
1. Regular (monomorphic) binary characters (e.g., 1st and 2nd). -The coding to be used for this type of characters is that obtained by deriving cumulative frequencies. This correspond to the second line of data for each taxon on the Nexus character matrix (labeled CumF). To select this you should go to the "Data" menu, select "Include-Exclude Characters...", and then "CharSets".
-For this particular example choose NoEvolStagesCumF and FrontLimbsCumF.
2. Ordered polymorphic multistate character (e.g., 3rdand 6th). -The coding to be used for this type ofcharacters is that obtained by deriving cumulative frequencies. This corresponds to the second line of data for each taxon on the Nexus character matrix (labeled CumF). To select this you should go to the "Data" menu, select "Include-Exclude Characters...", and then "CharSets".
-For this particular example choose EarHairsCumF, NoToesCumF.
3. Unordered polymorphic multistate character (e.g., 4th). -The coding to be used for this type of characters is that obtained by deriving noncumulative frequencies, since no assumption of order is assumed for the character states. This corresponds to the first line of data for each taxon on the Nexus character matrix (labeled Freq). To select this you should go to the "Data" menu, select "Include-Exclude Characters...", and then "CharSets".
-For this particular example choose DorsalColorFreq.
4. Autapomorphic binary character (e.g., 5th). -The program assigns a weight of 0 to all autapomorphic characters. For this reason they can be excluded from the analysis.
Note: All regular characters (monomorphic binary characters) should be treated as cumulative, with the cumulative set of subcharacters (a set of one per OTU).
