New Features and History of Changes

Here are some of the more notable new features and bug fixes since version 1.0. Bugs that would have yielded errors in substantive results (e.g. a bug in a phylogenetic calculation) are marked with .

Version 1.05

New Features

• added a new Find feature (in the Edit menu) that allows you to search for sequences within DNA data matrices. The first example of a module doing this is "Matching Sequence" which finds sequences matching a target sequence the user enters. The search allows a certain number of mismatches. Optionally, it can search for the reverse, complement and reverse complement of the target sequence.
• added a new item in the Select menu of Character Matrix Editor, "Select Lowercase Ends". This selects the ends of a DNA sequence up to the first block of N sites in a row with uppercase symbols. The user chooses N. Assuming that lowercase letters are used for less certain base calls, this can be used to select and then trim (by painting with gaps) poorly-sequenced terminal regions.
• the Concatenate Matrices command will now allow molecular sequence data to be concatenated to the end of a matrix of standard categorical characters.
• in the Mac OS X download, added an executable to run Mesquite under Java 1.4. This may be less stable than the standard version running under Java 1.3.1. The Java 1.4 version should be used only if you have Java 1.4.2 update 2 or later on Mac OS X. (The problems with early versions of Java 1.4 appear to be restricted to Mac OS X.)

Bug Fixes

• () fixed bug in the Brownian motion simulations of continuous character evolution. Brownian motion puts more change on long branches, less change on short branches. The bug in the simulations caused this contrast between long and short branches to be heightened — long branches had even more change relative to short branches than they should have. (Inadvertantly the effect of branch length had been squared in the calculation.)

Version 1.04

New Features

• added Utilities submenu to Tree menu of Tree Window. Currently there is only one utility, E-mail Tree, which prepares a text image of the tree and puts it in the body of an e-mail message requested using a web browser's mailto: command.

Bug fixes

• () fixed bug in two tree simulators, Uniform speciation (Yule) and Uniform Speciation with Sampling. In versions 1.03 and before, these failed to randomize tip labels, resulting in trees whose shapes matches the model's expectations, but whose particular relationships did not. Thus, in previous versions the taxa were added one at a time to a tree growing through time. For example, if there are 6 taxa, then the divergence between the 6th taxon and its sister species was always the most recent divergence in the tree. While this would not affect questions about general tree symmetry (e.g. "What is the distribution of tree asymmetries under uniform speciation?") or branch length distributions, it would affect questions about similarity between an observed tree and those expected under a null model of speciation.
• fixed bug that caused a crash when characters were deleted from a matrix which had annotations, images or colors attached to the cells but which didn't have footnotes.
• fixed a few minor bugs.

Version 1.03

New Features

• added automatic file backup, which retains copies of previously saved versions of files. This feature was added to allow the user to return to a previous version in case of errors or other problems. To enable this, in the Log window or Projects & Files window select Automatic NEXUS backup in the Defaults menu. Indicate the number of backups to be saved. If you enter, for instance, 3, then when you save a file named "myfile", the previous version of the file (if any) will be retained and named myfileBKP1. It will be in the same directory as myfile. The version before that will be called myfileBKP2, the version before that myfileBKP3. When you save the files again, the file ending in BKP3 will be deleted, BKP2 will be named BKP3, BKP1 renamed BKP2, and the newest backup will be called myfileBKP1.
• enabled grayscale shading in Trace Character History for continuous-valued characters. This can be turned on in the Trace menu by selecting the "Use Grayscale If Continuous" menu item.
• Matrices can be compared by selecting cells that differ. To request this, choose "Select by Matrix Comparison" from the Select menu of the character matrix editor. This is similar to the Utility "Compare matrices", but instead of giving a textual summary of the differences between two matrices, "Select by Matrix Comparison" highlights those cells of the matrix that differ.

Bug fixes

• fixed a bug that caused NOTES blocks to be written in duplicate form into all linked files (opened via Link File...) if all files were saved. This bug was generally innocent except if a linked file was subsequently unlinked from the main data file. This would leave the linked file with a relictual copy of the NOTES block. If the main data file was then edited (e.g., footnotes changed, characters deleted or moved), and then the secondary file was later linked again to the main data file, its relictual (and now out of date) NOTES block could override the current NOTES block in the main file. This could cause footnotes in the main data file to revert to former ones, or to be applied to inappropriate characters or taxa. In addition to fixing this bug, we have added a warning that is given if Mesquite detects that a NOTES block is being overridden. If you suspect that your footnotes may have been corrupted by this bug, please contact us for assistance.
• fixed a bug in Trees Directly from File that gave spurious warnings.
• fixed various other small bugs

Version 1.02

New Features

• multiple notes with images can now be associated with taxa, characters and cells of character matrices. Prior to 1.02 a single image could be associated with each taxon, or a single footnote could be associated with each taxon, character or cell of the matrix. Now, multiple notes can be attached to each taxon, character, or cell of a matrix. Each note can have a comment, a reference, an image, and an author. Labels can be attached to the image. To use this, select the notes tool () in the Character Matrix Editor. If you touch on a cell, a Annotations window will appear with the notes for that cell, if any. Buttons in this window can be used to delete and add notes and images, and to make additional notes windows. Behavior of the window can be modified using its Annotations menu. NOTE: the single footnote system still exists and is independent of this multiple notes system.
• MRP matrices can be generated from a set of trees, for use by Matrix Representation with Parsimony analyses to construct supertrees. To use this, select MRP Matrices from trees as a source of matrices (e.g., under Characters menu, Make New Matrix submenu, Other Choices).
• a search facility has been added to the Character Matrix editor and to the List windows. The cell of the matrix found by the search is highlighted and made visible. To use this, select Find String or Find Footnote from the Edit menu. Find String searches through the row names first (e.g., taxon names for the Character Matrix Editor), then the column names (e.g., character names), then the internal cells of the table (e.g., the character state codings). Find Footnote searches the footnotes of the Character Matrix and highlights cells containing the requested text in their footnotes. You can also search for stretches of sequences or state distributions matching the currently selected stretch using Select Same Sequence and Select Same Distribution of the Select menu of the Character Matrix Editor.
• More choices were added for coloring character matrices. Both text and background of a cell can now be colored according to properties of the cell. A paintbrush tool () was added to allow arbitrary coloring of cells of a character matrix.
• taxa and characters can be moved by a menu item "Move Selected [taxa or characters]To..." in the List of Taxa and List of Characters windows. Prior to 1.02 taxa and characters could be moved by clicking and dragging, but using this it was difficult to move them long distances through a matrix. To use this, select the taxa or characters to be moved in their respective List window, and select Move Selected from the List menu.
• Taxon selecting in the tree window has been modified, with a new taxon select tool ().
• Utilities to modify taxon names have been enhanced and added to the Character Matrix Editor in the Taxon Names submenu of the Matrix menu.
• Added import/export of FASTA files

Bug Fixes

• () fixed calculation of Shared Partitions, which counted too many shared partitions between trees in some circumstances if the trees had different terminal taxa included
• resolved conflict in interpetation of tree descriptions that would result in Mesquite's interpreting trees from MrBayes and other programs as having reticulations whenever labels for internal nodes were duplicated. Mesquite now interprets these labels as cosmetic only, and hence not as indicating reticulations
• fixed bug involving the State Names Editor, by which a character might mistakenly receive a name duplicated from another character
• fixed bug in moving taxa or characters by dragging past the end of the matrix
• fixed bug in recoding characters by which state names and footnotes would not be adjusted
• fixed various other small bugs

Version 1.01

New Features

• added on-the-fly filtering and transforming of trees. Thus, trees being supplied from a file or simulation can be filtered according to various criteria or can be transformed with the available tree or branch length alterers. To use this, whenever a source of trees is needed, choose first "Filter Trees from Other Source" (if you want to select trees satisfying a criterion; more details here) or "Transform Trees from Other Source" (if you want to transform trees, e.g. reroot, scale branch lengths, etc.; more details here), then indicate what source of trees is to be filtered or transformed, and what filter or transformation is to be used.
• added module to read trees directly from a file one at a time; allows processing of much larger tree files (>50,000 trees). To use this, request "Trees Directly from File" as your source of trees for charts and other calculations. You can also build a tree block from a sample of trees from a large file by selecting "Include partial contents" from the "Get File With Trees" submenu of the Taxa&Trees menu.
• available tree and branch length alterers can be applied to all trees in a tree block. To use this, go to the Utilities submenu of the List menu of the List of Trees window.
• added a new tree alterer: outgroup rerooting of trees. To reroot trees using a selected set of outgroups, you first must select the outgroup taxa, then, choose the menu item "Root tree with selected taxa as outgroup", for instance in the Alter/Transform Tree submenu of the Tree menu of the tree window. More details are given on the page on trees.
• added integrated BLAST search. To use this, go to a character matrix editor window showing a molecular matrix. Select one or more stretches of sequence and choose BLAST Search from the Search submenu of the Matrix menu. Mesquite will then send a request to your web browser to perform a BLAST search at NCBI's BLAST server, one request for each of the selected stretches of sequence. The results will be available in your web browser.
• added -w (windowless) and -b (backgroundable) flags for running long Mesquite jobs in the background in Unix from the command line
• improved user interface of tables (List Windows, Character Matrix Editor), including navigation with arrow keys and more informative explanations and footnotes
• Added autotab to the Character Matrix Editor. With this, the edited cell shifts automatically to the right or downward when a state is entered. To use this, select the Select and Type tool (with the letter "K") and use its drop down menu to indicate autotab right or autotab down. Autotab functions only when the Select and Type tool is the active tool.
• selection of taxa, characters and trees is now remembered when files are saved
• calculations of charts and Trace Character Over Trees can now be stopped part way to show partial results

Bug fixes

• fixed tree printing bug by which node numbers and branch lengths always appeared
• fixed bug by which pressing the Delete key while editing in a table would be misinterpreted as a requesting to delete a character, taxon or other object
• fixed bugs in NEXUS file reading and writing (concerning SYMBOLS list, blank character names, tokenization with tab or square brackets, near-duplicate taxa blocks in same file)
• fixed bugs in State Names Editor and Character Matrix Editor concerning footnote display and editing
• fixed bug with Mac OS X 10.3 by which dialog boxes with lists always chose first item (this was not a bug in Mesquite, but rather in Mac OS X, but we have found a workaround)
• fixed bug with Windows by which pie diagrams would be misdrawn as entirely black for traced characters in the Balls and Sticks tree drawing mode (this was not a bug in Mesquite, but rather in Windows/Java, but we have found a workaround)
• several other smaller, less notable bugs were also fixed