FAQ

=Mesquite FAQ=

How do I find the most parsimonious tree in Mesquite?
Mesquite is not designed for rigorous tree searches, but it can perform NNI and SPR tree searches. To search for the most parsimonious tree(s) for a character matrix, select Taxa&Trees > Make New Trees Block from > Tree Search > Heuristic (Add & rearrange). If you have more than one block of taxa in the file, you will be asked to choose the block of taxa you would like to perform a tree search for. Select "Treelength" as the criterion for the tree search. Select "Current Parsimony Models" as the source of current parsimony models. You have two options for the rearranger to use: NNI or SPR. NNI (Nearest-Neighbor Interchange) generally produces a tree faster than SPR (Subtree Pruning and Regrafting), but NNI has a greater chance of failing to find the most parsimonious tree(s) than SPR. You will be prompted to set the maximum number of equally good trees to store during search (MAXTREES). Increasing MAXTREES will result in an increase in search times, accompanied by a greater probability of finding the most parsimonious trees (and lower settings of MAXTREES will result in quicker, but less thorough treesearches). If multiple character matrices (for the Taxa block you are performing a tree search for) are included in the file, you will be prompted to choose the character matrix to use for the tree search. Once the tree search is complete, you will be asked if you would like to open a window to view the trees.

How do I show the length of a tree?
Begin by opening a New Tree Window for the tree you are interested in. From this tree window, select Analysis > Tree Legend... Choose "Treelength" as the information to be displayed in tree legend. Select "Current Parsimony Models" as the source of current parsimony models. If multiple character matrices (for the Taxa block you measuring Tree Length for) are included in the file, you will be prompted to choose the character matrix to use for the tree length. The tree length will shown in the legend that opens in the tree window.

How do I trace a character on a tree?
Tracing the evolution of a character is not entirely trivial, and depends on a variety of choices you make, including which characters to trace, the method of character reconstruction (e.g.,parsimony, likelihood, stochastic character mapping), etc. Here we provide brief instructions on reconstructing a single character on a tree, but we encourage you to read more about the details of Tracing Character History. Begin by opening a New Tree Window for the tree you are interested in. From this tree window, select Analysis > Trace Character History and "Stored Characters" as the source of characters to reconstruct. (If you have "Use Stored Characters/Matrices by Default" turned on in the Defaults submenu if the File menu, Mesquite won't ask you and will simply use Stored Characters.) You will then be prompted to choose the reconstruction method. Parsimony models can reconstruct ancestral states for continuous and categorical data, including molecular data, while Likelihood and Stochastic Character Mapping methods can currently only be used for (non-molecular) categorical data. If you are using Likelihood or Stochastic Character Mapping as the reconstruction method, select "Current Probability Models" as the source of current probability models. If multiple character matrices are included in the file, you will be prompted to choose the character matrix to use as the source of characters to trace (Note: Mesquite will provide a list of all the character matrices for the corresponding Taxa block, including those for which models of character evolution are not currently available in Mesquite; e.g. even if you have selected "Likelihood" as the Character Mapping method, molecular and continuous Character Matrices, if they are present in the file, will be listed.). Choose the desired character matrix, and the first character will be traced on the tree. To scroll between characters, use the arrow on the Trace Character legend. For molecular and Categorical characters, you can change the colors of character states by double-clicking on the colored box in the Trace Character legend. Default colors for character states can be restored by selecting Trace > Revert to Default Colors Additional information on the tools found in the Trace menu can be found in the Mesquite manual under the Trace Character History section.

How do I analyze population structure using Slatkin & Maddison's s statistic?
We strongly urge you to read about population genetic tools in Mesquite, especially the section containing an example using Slatkin & Maddison's s statistic to test hypotheses concerning divergence times. There is also a guide which provides basic step-by-step instructions on performing this type of analysis. Additionally, the paper describing the statistic (Slatkin & Maddison, 1989, Genetics 123:603-613) is highly recommended reading.

How do I create a publication-quality tree?
Mesquite is not designed for rigorous tree-estimation procedures, such a Maximum Parsimony, Maximum Likelihood, or Bayesian tree estimation. However, trees generated from programs such as PAUP, PHYLIP, and MrBayes can be read into and manipulated in Mesquite. This guide to producing quality trees will help you perform these manipulations to create a tree suitable for scientific publication.