Publication+Quality+Trees

=Publication Quality Trees= 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 will help you perform these manipulations to create a tree usable for scientific publication. Users should begin by familiarizing themselves with the [|Mesquite file structure].

Step 1: Get a tree
> Importing trees from files can be done through Taxa &Trees > Import File with Trees... menu option. To include the trees in the Mesquite file, select "Include Contents...". Alternatively, you may open a Tree Window corresponding to trees from external sources from Taxa&Trees > New Tree Window by selecting "Use Trees from Separate File" as the source of trees for the new Tree Window. > Note: if you are importing trees from PAUP, and would like to retain the branch lengths, you must be sure to save the branch lengths from within PAUP. From the command line in PAUP, use the brlens = yes option in the savetrees command. If you are using PAUP with menus, you can save the branch lengths when saving the tree (Trees > Save Trees to File...) by clicking on the Options... tab and checking the box Include branch lengths. If you want Mesquite to display bootstrap values generated by PAUP, then in thesavetrees command use savebootp = brlens option; in the version of PAUP with menus, use the Options... tab and ask to save bootstrap proportions as branch lengths.
 * Within Mesquite — Mesquite can provide trees from simulations, some basic tree searches, or default trees. If you do not have trees from other sources, you can open a tree window from the Taxa&Trees menu by selecting New Tree Window. If you have multiple taxa blocks in the file, you will be prompted to choose among the blocks included in the file. You will then be asked to choose a tree source. There are at least 13 different sources for trees, but we will only deal with the first two here. "Stored Trees" refers to trees that are stored in the Mesquite file. If you haven't stored any trees in the file yet, this option won't be available. Selecting "Default Trees" will open a Tree Window corresponding to a Tree Block with three trees: a fully resolved symmetrical tree (Default symmetrical), a completely unresolved tree (Default bush) and a ladderized tree (Default ladder) (the names of trees are shown in the panel beneath the the tree). You may manupilate any one of these trees, but be sure to store a copy of the tree in the Mesquite file (Tree > Store Copy of Tree As...), or it will be lost.
 * Other sources — When importing trees from other files, be sure that the taxon names from the tree file match the taxon names in the Mesquite File. Although importated trees may contain fewer taxa than are in the Taxa Block, they cannot contain taxa that are not included in the Mesquite file. If the trees you wish to import contain taxa that are not represented in the Taxa Block you should either (1) add those taxa to the correspondidng taxa block in Mesquite ( List > Add Taxa... from Taxa Window) or (2) delete those taxa from the tree file before importing them into Mesquite. We recommend the former (adding Taxa to file), in order to reduce the probabilty of inadvertantly altering tree structure.

Step 2: Choose Tree Form
Some examples of Tree Forms: Most trees are published as "Square Trees", which you can select from the Display menu in the Tree Window. There are a variety of other formats available, which we encourage you to explore, but some of the following instructions will only apply to square trees (this is noted where it applies).
 * [[image:http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/Help/images/diagonalTree.gif width="144" height="170" align="center"]] || [[image:http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/Help/images/squareTree.gif width="144" height="170" align="center"]] || [[image:http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/Help/images/curvogramTree.gif width="144" height="170" align="center"]] || [[image:http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/Help/images/ballsNSticksTree.gif width="144" height="170" align="center"]] ||
 * Diagonal || Square || Curvogram || Balls N Sticks ||

Step 3: Branch Lengths
To show branch lengths of a tree, select Display > Branches Proportional to Lengths. The branches will now reflect lengths, and a scale is shown. You can toggle the scale off/on from the Display menu (Display > Show Scale). Note: if the branch lengths for a tree are unassigned, and Branches Proportional to Lengths is selected, the tree will be drawn with arbitrary branch lengths (usually so that each branch has a length of 1.0) and the scale shown. If you don't know if the tree has branch lengths assigned, see the instructions for viewing the tree in [|newick] format, below. Alternatively, you can check branch lengths by using the "Adjust Branch Length" tool ; if a branch does not have a branch length assigned, the box that opens when you use the Adjust Branch Length tool will show a "?".

Step 4: Branch Colors
There are two approaches to coloring branches, the first colors all branches of the tree, and the second applies different colors to different branches (there is a third means of coloring branches, according to Character Reconstructions, but for this step, we only discuss the first two). To color all the branches of a tree, select Display > Branch Color and choose from the list of available colors. To color individual branches, you can use the Branch Coloring tool from the Tree Window tool palette on the left-hand side of the Tree Window. This tool can be used to add colors for cosmetic effect to a tree (these colors play no role in analyses, and are not dictated by character states per se. See "Character Reconstructions" under step 6 below for branch coloring that based on character reconstructions). To set the color, right/control-click on the Branch Coloring tool icon, select Branch Paint Color, and choose from the list of available colors. Clicking on a branch with this tool will color that branch, control-clicking on a branch will color that branch, and all the descendant branches. You can remove colors from branches by right/control-clicking on the Branch Coloring tool icon, and selecting Remove Color. The Remove Color tool works the same way as the branch coloring tool on single branches (click) and entire clades (control-click). You can also remove all colors from a tree by selecting Remove All Color from the Branch Coloring Tool icon options. It is important to note that colors added with the Branch Coloring tool will always be on top - any color changes applied from the Display > Branch Colors will not be visible on branches that have been colored using the Branch Coloring tool.

Step 5: Taxon Name Colors
To color taxon names, you can partition the taxa into groups (groups are not the same as [|associations]. To set a group, first go to the Taxa window for the Taxon block that contains the Taxon names you'd like to color (this will be the taxon block that corresponds to the tree window you are looking at). There should be a "Group" column on the list. If not, you can show the column by selecting Columns > Group Membership (taxa). First, select all the taxa in your first group. Using the small black triangle at the top of the column, select New group... (clicking once on the black triangle will bring up the Group menu). In the New Taxon Group dialog, type a name for this Group, and select a color. From the Group menu (accessible from the top of the Group column), you can create additional new Groups, edit current Groups, and set Group membership. For the latter, select the taxa you wish to place in the group, and selectSet Group > from the Group menu (the list of groups is shown). Each taxon can only be assigned to a single Group. The taxon names in the Tree Window should be the same color as assigned to the Group. If they are not, you can color them so by selecting, in the Tree Window, Display > Names > Color by Taxon Group. Alternatively, you can color the background of the taxon text by taxon group by selecting Display > Names > Background Color by Taxon Group. Of course, you'll likely want to turn off Color by Taxon Group, or the names will be the same color as the background, and thus won't be visible! Because taxa can only be assigned membership to one Group, if you would like to draw more than one tree, which differ only in Taxon Name coloration (topology and branch lengths being the same), it would be easiest to draw the tree first with one set of Group memberships, then save the file under a different name, and in the new file, change the Group memberships. This will make it easier to assign different Group memberships without overwriting other desired memberships.

Step 6: Extras
> For example, this tree, > > in newick format, lacking branch lengths, would be: > > ((A, B)100, C)75 > The same tree, if it had branch lengths of 10 and 5 for clades AB and ABC respectively: > > ((A, B)100:10, C)75:5 > If the tree does not show support values, you will need to enter them using the Node Namer tool. The default position for support values is on the node of the tree; however, published phylogenetic trees usually have support values centered on the branches. If you are using a Square Tree, you can center the support values on a branch by selecting Display > Names > Center Branch Names (note: this option is currently only available for Square Trees). If the support values overlap (this will be an inevitability as the number of taxa & support values increases), you will need to save the tree in pdf format (step 7 below) and use a graphics editing program (Illustrator, Photoshop, etc.) to correct the overlap. > > If the branch labels are not in the format you would like (for example, they are shown as decimal values from 0.0 to 1.0, but you want them to be percentages from 0 to 100), then you should convert them to branch lengths first, which would then give Mesquite the option to change how the numbers are displayed. To convert them to branch lengths, choose Tree > Alter/Transform Branch Lengths >, and in the dialog box that appears choose Assign Branch Lengths from Node Names. You can then show the values using the information provided in the next section.
 * Support Values as Branch Labels - If you would like to add support values to your tree, there are different ways to do so, depending on how you initially got the trees. Some programs save values as branch labels, then this section applies (if they program saves values as branch lengths, then see the next section). Bayesian trees from MrBayes usually contain the posterior probabilities, so they should be visible when you load the trees into Mesquite. If they are not, and the posterior probabilities are in the tree in Newick format, you can turn them on by selecting Display > Names > Show Branch Names. If you're not sure if the support values are in the Newick format tree, click on the "Text" tab in the Tree Window. You will see the line "Tree Description", which shows the tree in Newick format. If the support values are present, they will be evident as a string of characters immediately following the right parenthesis of a clade.
 * Support Values as Branch Lengths - If support values are saved as branch lengths (for example, if you used the savebootp = brlens option in the savetrees command to save the tree resulting from a bootstrap analysis in PAUP), then you can see the values on that tree in the tree window by choosing Display > Branch Length Labels > Show Labels.The Branch Length Labels submenu allows you to adjust how the values are displayed, including the number of decimal places (for standard bootstrap values, you might wish to change this value to zero), whether or not the terminal branches have values displayed, and the color of the label. If the values are shown from 0.0 to 1.0, but you wish to change them so that they show percentages, you can multiply all values by 100 using Tree > Alter/Transform Branch Lengths > Scale All Branch Lengths....
 * Character Reconstructions - You can trace character reconstructions on trees by selecting Analysis:Tree > Trace Character History. Most likely, you will be tracing Stored Characters. Note that tracing a character history will "fill" the branches with a particular color, so that any colors added using the Branch Coloring tool or the Branch Color menu item in the Display menu will only outline the branch. [|Studying the History of Character Evolution] has more detailed information regarding ancestral character reconstruction, and additional instructions may be found in the [|Mesquite FAQ] page.

Step 7: Exporting the Tree
When you're satisfied with the tree in the Tree Window, select File > Save Tree as PDF... (you can add the extension ".pdf" when you save the tree. Mesquite will not do this automatically, but applications capable of reading pdf files will still be able to open it without the extension).