Known Bugs in MacClade 4

David R. Maddison and Wayne P. Maddison
25 July 2005

Here is a list of the known bugs in MacClade 4. Many more minor bugs are not included. Bugs marked with may affect the numerical results presented by MacClade. The names of those who reported each bug (if someone other than DRM and WPM) are given in parentheses after the description. If you do not have the latest version of MacClade 4, check out the updater page.

The most recent release version is 4.08.

General

Description	Versions with bug	Version with fix
The "File Notes" and "Notes about Trees" windows are not available	4.02	4.03
Under MacOS X, MacClade will at times believe there is not enough memory available to perform a task (such as reading in a large file, or displaying a very large tree), even when there is sufficient memory. (Jonathan Marcot.)	4.04	4.05
If you ask MacClade to open a file with many more than the allowed number of characters (that is, much greater than 32,000), the error message was not appropriate.	4.0-4.06	4.07
MacClade would fail to deal with very large files or matrices on MacOS X and give an incorrect "Out of Memory" message. (Zack Hyde).	4.0-4.07	4.08

NEXUS file reading/writing

Description	Versions with bug	Version with fix
With nucleotide data, if some sites are set as "coding, undesignated", this is not saved by MacClade when the file is written. (Hervé Sauquet.)	4.0	4.01
If some taxa have single quotes in their names, and MacClade tries to read TREE commands in which full taxon names are entered in the tree description, the tree will not be read properly. This occurs with consensus files written by PAUP, for example. (James Albert.)	3.0-4.03	4.04
Foreign NEXUS blocks with more than 32,767 characters will not be saved properly in a file.	4.0-4.04	4.05
If two tokens in the file differ only by characters that are exactly 32 ASCII values apart (e.g., 2 and R) but at least one of these is NOT a letter, MacClade will falsely consider those two tokens identical. (Bill Piel.)	4.0-4.07	4.08

Import/export

Description	Versions with bug	Version with fix
Importing NBRF sequences into MacClade failed if the file was saved on a Microsoft Windows machine rather than a MacOS machine.	4.0	4.01
Under some circumstances some elements of a NONA file will not be imported. (Kip Will.)	4.0	4.01
Some common forms of GCG/MSF files that violate the official GCG/MSF file format cannot be read by MacClade. (Richard Thomas.)	4.0	4.01
Some other common forms of GCG/MSF files that violate the official GCG/MSF file format cannot be read by MacClade. (David Posada and Steve Perlman.)	4.0-4.01	4.02
NBRF sequences imported into MacClade had the first character of each sequence removed. (Jonathan Marcot.)	4.01	4.02
NBRF files with no text in the comment lines can have the first part of each sequence removed. (Byron Adams)	4.01	4.04
NBRF files with an asterisk in the comment lines failed to read.	4.0	4.06
GenBank files containing a URL in the text failed to read.	4.0-4.07	4.08

Data editor

Description	Versions with bug	Version with fix
The Codon Splitting Cost feature of the pairwise alignment tool does not always work.	4.0	4.01
Under rare circumstances MacClade may crash if the column width is changed.	4.0	4.01
Some tools in the editor were not available if all characters were selected or if the clipboard contained as many characters as in the matrix. For example, the Stamp Clipboard tool did not work if an entire sequence was in the clipboard. (Aniko Sabo.)	4.0	4.01
The Display menu did not always contain all relevant items when the data editor was frontmost. (Margaret Thayer.)	4.0	4.01
MacClade would often crash, or have other odd behavior, if you selected entire characters by touching on the character numbers at the top of a column, and then used the Selected Block Mover tool on them.	4.0	4.01
Choosing Undo in the editor after having converted nucleotides to amino acids resulted in a crash.	4.0	4.01
The Condense Taxon Names feature sometimes did not generate unique taxon names. (Tomoaki Nishiyama.)	4.0-4.01	4.02
Find String won't find a string of bases if they are at the start of a sequence, and that sequence's name is selected. (Bill Piel.)	4.0-4.01	4.02
The pairwise alignment tool will attempt but fail to align data if you have set all alignment costs to 0. (Byron Adams.)	4.0	4.04
The pairwise alignment tool would occasionally crash.	4.0	4.06
Inserting large numbers of characters into the matrix occasionally caused a crash.	4.0-4.06	4.07
Taxon Sets were inadvertantly removed from the Consensus Taxa submenu	4.04-4.06	4.07
Printing the data editor failed. (Ian Frame.)	4.06	4.07
Under rare circumstances the pairwise alignment tool would add an extra base to the end of a sequence. In so doing, it would give an error message alerting the user to the problem, so this should not have caused data corruption. (Heidi Döring.)	4.0-4.06	4.07
If you import sequence data into a file, then later add empty taxa from within MacClade, then choose Undo, both the empty taxa and the imported sequences would be removed.	4.0-4.06	4.07
The state name for the 26th state in Extended Standard data would not display properly in the data editor. (Alessandro Mosco.)	4.0-4.07	4.08
Recode crashes on occasion with molecular data.	4.0-4.07	4.08

List windows

Description	Versions with bug	Version with fix
If the name of an object was selected in a list window, and the list window was resized, the name of the selected object was sometimes drawn over top of the wrong row. (Michel Laurin.)	4.0	4.01
The number of taxa shown in the Trees List window is sometimes incorrect if taxa newly added to the matrix are newly added to a tree. (Michel Laurin.)	4.0	4.01

Assumptions

Description	Versions with bug	Version with fix
If exactly two characters are selected in the data editor, and the Change Weights menu is used to change their weights, only the weight of the first one will be altered.	4.0	4.01

Tree window

Description	Versions with bug	Version with fix
If the tree legend is locked, deselecting the checked items in the sigma menu does not make them disappear from the legend. Only if the legend is unlocked will it update. (Bill Piel.)	4.0	4.01
In Trace All Changes mode, with changes shown using bars, and with bar shape indicating what the character does elsewhere in the tree, IF a unique apomorphy of a clade was unchanged above the branch, but if some taxa in the clade had missing data for that character, then the bar was shown as "changed above, not outside" when it should have been marked "unique, uniform above".	4.0-4.03	4.04

Charts

Description	Versions with bug	Version with fix
MacClade will crash in some circumstances if you grab the scroll bar's thumb button in the table view of the Compare 2 Trees chart.	4.0-4.01	4.02
The log file for some of the State Changes & Stasis charts has confusing, unlabelled output	4.0-4.03	4.04