MacClade 3 Bug List
Wayne P. Maddison and David R. Maddison
14 August 1996
Here is a list of the known bugs in MacClade 3.
Unless otherwise stated, bugs fixed in version 3.0x of MacClade
were present in version 3.0 through 3.0x-1. (For example, most bugs
fixed in version 3.03 were present in versions 3.0-3.02.) Unless
otherwise stated, the bug was found by us and has not been reported
by a user. Bugs marked with
may affect the numerical results presented by MacClade.
Bugs fixed in 3.01
For molecular sequence data, if States chart on screen, and data
file saved, then first line in textual summary of chart will be
bogus until you ask to have the chart recalculated. Bug in version
- If you copy to the clipboard entire rows and columns from the
data matrix, then select entire whole rows and columns that
contain different numbers of taxa and different numbers of
characters than those in the clipboard, and try to paste, MacClade
will rightly refuse to paste the data, but it will incorrectly add
new rows or columns or delete old rows and columns in the process.
Bug in version 3.0.
For protein data matrices, if you are in the treewindow, and ask
for Type Edit under Assume, then press the New button, and choose
"Protpars type based on genetic code", and press Create, MacClade
will create a protein parsimony user-defined type. However, there
may be amino acids in the matrix that are not present in the
current genetic code (e.g., an amino acid specified as serine (S),
but not specified as to which type of serine (1 or 2) in the
standard nuclear code). MacClade would then present you with the
query "AAs not present in genetic code found in matrix: do you
wish to convert these to the appropriate AAs?" If you choose to
convert, then various statistics, including traced characters,
various charts, and so on, will not be updated. To have them
recalculated properly, return to the data editor, and then go back
to the tree window.
- If you ask to Recode a character in the editor, and Footstates
is turned on, then the footstates will not be updated after the
- Some of the functions for adding taxa and characters in the
editor allowed you to expand the matrix beyond the allowed 1500
taxa and 16000 characters.
- If you created new user-defined types in the Type Edit dialog
box, but pressed Cancel to exit the dialog box, MacClade will
remove the newly-created types, as expected. However, the next
time you choose the Type Edit dialog box, MacClade may crash. This
crash can be avoided if you trace a character in the tree window
before you call Type Edit the second time, or if you select one
entire character in the data editor just before calling Type
Bugs fixed in 3.02
- Taxon, character, and state names cannot consist entirely of
numbers. MacClade mistakenly allowed names that consisted of
number followed by blanks or underscores. Bug reported by one
- If you copy a complex picture (perhaps a color image) to the
Clipboard in another program, then switch to MacClade, MacClade
may crash if that picture takes more than 32K of memory.
- There were a few minor problems with the vertical positioning
of the tree in the treewindow and the vertical scroll bar in some
circumstances, especially when Data Boxes were turned on. This
occasionally resulted in one part of the tree appearing at a
different level than another part.
- If taxon labels in the tree window were any style other than
plain (that is, bold, italics, etc.), then the labels for the bars
on branches in Trace All Changes mode were also mistakenly of this
- If you used the drag-and-drop rerooting tool, and touched on a
branch, but did not move the tool off the branch before you let go
of the mouse button, MacClade would crash. Bug reported by three
- On occasion MacClade would query you to save a tree file when
closing a data file, even though no tree file was open.
- On a Macintosh with a 16 or more colors or grays shown,
MacClade occasionally incorrectly printed Data Boxes.
If Trace All Changes is shown, with Minimum and Maximum changes,
and you went to Print Tree, and choose Multiple Trees from the
Options pop-up menu, then asked to print multiple trees, MacClade
would incorrectly show changes on the printed trees, and would
give some error messages. Bug reported by two users.
- If you asked to not show the trace legend in Print Tree, this
request was forgotten the next time you invoked Print Tree. Bug
reported by one user.
- If you asked to print Data Boxes from within Print Tree,
printing might not take place until you left the Print Tree dialog
- On occasion the preview image in the Print Tree dialog box was
not updated correctly. Bug reported by one user.
- If a data file in MacClade 2.1 format contained an invalid
tree description, with one taxon occurring more than once,
MacClade 3 would usually crash upon reading the file or displaying
the tree. Bug reported by one user.
- In Trace All Changes, if the number of changes varied by less
than 10 across branches, but the maximum number of changes on any
branch is greater than 10, and if the trace was indicated with
patterns or colors, then the legend would incorrectly label the
patterns or colors.
- In the Character Steps/etc. chart, if one chooses the chart
with number of steps on the vertical axis and character number on
the horizontal, and changes the interval width to something other
than 1 (see pp. 276&endash;277 of the MacClade book), then
MacClade may crash if the number of characters is not divisible by
the interval width. Bug reported by one user.
- If you modify the Evolve Segments of various branches, then
save the file, there are occasions in which the number of segments
of the right-most branch on the tree will be incorrectly set on
re-opening the file. Bug present only in version 3.01.
- Occasionally a scroll bar will be incorrectly drawn in the
textual summary of a State Changes & Stasis chart. Bug present
only in version 3.01.
If a chart is on the screen, and Evolve Characters is invoked, and
there are fewer states per character in the simulated characters
than in some of the original characters, then the chart may be
drawn incorrectly, omitting some of the higher-valued states.
- When an observed taxon is fixed as ancestor then holding the
cursor over the corresponding internal branch should cause the
message box to indicate the taxon's name, but instead it indicates
garbage if the internal branch is a left-leaning branch.
Whenever the State Changes & Stasis chart was used and
observed taxa were fixed as ancestors, the chart gave false
results. The results included ficticious changes that varied
haphazardly according to situation.
- In printing Char. & State Names from the Print Other
submenu, the last character listed on each page may have some
states omitted from the list. Bug reported by one user.
In printing Branch Lists from the Print Other submenu, all pages
after the first may have the first line of the page printed at the
bottom of the page, thus giving the incorrect impression that a
character changes along the branch listed at the bottom of the
page, rather than that listed at the top of the page. Bug reported
by one user.
In Trace All Changes, if branch lengths are weighted, and if
decimal-valued weights or user-defined types are in use, then in
Print Tree, if you choose to show the scale of the branch lengths,
then the scale will be labeled incorrectly.
Bugs fixed in 3.03
- On rare occasion, MacClade will refuse to open files from the
Open File menu item. This seems to be restricted to hard disks
that have been extensively used since last formatted, and that use
System 7. Bug reported by six users.
- For Extended Standard or protein data files, if Type Edit
opens to display a step matrix type with 8 or less states, and you
then display a type with 10 or more states, the scroll bars will
overlap part of the step matrix. Bug reported by one user.
Bugs fixed in 3.04
- If Minimum-Average-Maximum Trace All Changes is shown on a
tree, and you go to Print Tree and have the tree drawn with branch
lengths proportional to number of changes, and ask to print Data
Boxes, the taxon names will be printed in the incorrect place. Bug
reported by one user.
- If a taxon has footnotes attached to more than one of the
characters, then MacClade may fail to print some of these
footnotes if they appear near the bottom of a page. Bug reported
by one user.
- In the Print Tree dialog box, if you click on the Print Tree
button, but then click on the Cancel button to avoid printing,
MacClade may perform some unnecessary calculations.
- There were times in which symbols for gaps, missing data,
etc., could conflict with those for character states, but MacClade
would not provide proper warning. For example, with a DNA data
file, you could designate a gap as 'Y', which would conflict with
the symbols list used by MacClade for the Genetic Code dialog box,
causing it to be displayed incorrectly. Bug reported by one
- The CHARSET command in the ASSUMPTIONS block of a NEXUS file
was occasionally misread, resulting in either a crash or very
sluggish performance. Bug reported by one user.
- If you Save Preferences in the Symbols dialog box for standard
or extended standard data files, then set the default data format
preference to DNA, RNA, or protein, then any new file you create
will be designated as DNA, RNA, or protein, but will have
incorrect state symbols.
- In some circumstances, touching just below the column width
control in the data editor would cause MacClade to crash.
- Some options in the Trace Labeling dialog box were not saved
as preferences properly for Trace All Changes.
- There were some problems in screen display in the Include
Exclude Taxa dialog box.
- In exporting polytomous trees to Hennig86, MacClade would
incorrectly give a warning that the polytomies in the trees were
- With a continuous character traced, the trace legend would use
as its range for shading the entire range of states on the whole
tree. However, the trace would use as its range that on the
currently shown clade. Since the ranges determine the assignment
of shades/patterns to states, the trace could therefore disagree
with the legend when a clade was expanded on the screen. This was
fixed by using range on whole tree for both Trace Continuous and
Trace All Changes (since adjustment to expanded clade was deemed
- If one imported a foreign file format in which some characters
were specified as not being of default type for that file format
(e.g. a Hennig86 file with some characters being unordered), then
when that file was saved within MacClade, the current typeset was
occasionally saved incorrectly (e.g. a Hennig86 file may have been
saved with all character ordered).
- Switching the number of significant digits for indices such as
the retention index was not immediately reflected in the screen
Bugs fixed in 3.05
- PHYLIP 3.4/3.5 data files that contained trees were written
incorrectly. After the data matrix, but before the trees, a line
is supposed to be included containing the number of trees. This
line was not written into the files.
- If you tried to import some files as MacClade 1.0 or 2.1
files, when in fact they were files of another format (e.g.
PHYLIP), then MacClade would occasionally crash. Bug reported by
- Some files (e.g., in simple table format) in which there were
several carriage returns or linefeeds after the last character
state symbol could not be imported into MacClade.
- When a taxon was deleted from the matrix, the trees stored in
memory were sometimes adjusted incorrectly for the deletion of the
taxon if the taxon had been placed as arising out of a polytomous
node (and certain other conditions held) [namely, in the
polytomy's "ghost" resolution, the taxon is at the base of the
- If the number of text characters contained in all of the
footnotes stored in a data file exceeded 32,000, the footnotes can
become corrupted. Bug reported by three users.
- If Track Cell was turned off in the Edit menu in the data
editor, then text characters typed into the cell of a taxon or
character name were not displayed immediately. Bug reported by one
- The character sets written in TYPESETs, WTSETs, and similar
objects in the NEXUS file were occasionally written in a redundant
fashion in protein-coding nucleotide sequences.
- Names of user-defined character types that contained a period
('.') were occasionally altered by MacClade.
Weight sets, type sets, inclusion sets, character sets, and codon
positions are saved incorrectly for DNA and RNA sequence data if
these sets have odd patterns (for example, if sites 1, 3, 4, 7, 9,
10, 12, 13 were excluded, this would be saved incorrectly, but if
every third site were excluded,this would be saved properly). This
may lead to incorrect results if the altered assumptions are not
noticed. Bug present only in version 3.04. Bug reported by one
If a block of cells is moved toward the start of the matrix in the
data editor (using the Block Moves feature), and is moved off the
start of the matrix (by holding down the Option key), and if the
characters that are moved off of the matrix contain no data (e.g.
are all missing), then the remaining cells moved in the block will
be reassigned the state present in the highest-num ber charactcer.
(We know this sounds complicated, but you would know it if it
happened to you!) Bug reported by one user.
- If the tree on the screen has been given a name, and then
different branch segments are assigned to the various branches,
and the file saved, the branch segment information will be lost
when the file is reopened.
- On Mac 660AV and 840AV's, MacClade will on occasion present
the user with a -35 error, and will refuse to open many files
subsequently. Reported by four users. This is the "Stern AV Bug",
which took about 7 months to track down; thanks to David Stern for
his heroic efforts in helping us figure this one out.
- If you have user-defined types, and then change the format of
the matrix (e.g. from standard data to DNA data) in such a way
that the maximum state number in the new matrix is less than that
present in the user-defined type, then MacClade may crash if you
subsequently choose to edit types.
Bugs fixed in 3.06
- If you read in a NEXUS file that has a data matrix with states
represented by numbers other than 0 and 1, but that does not
contain a FORMAT statement in a DATA or CHARACTERS block, then
MacClade will incorrectly display the states in the data editor
using some odd symbols, such as boxes. Bug in versions
- The Search and Replace feature was inadvertently disabled in
- With DNA or RNA sequence data, the program would sometimes
save weightsets, typesets, etc., with bogus character numbers
(specifically, it would save the weight for a non-existent
character). This shouldn't cause any significant problems, other
than making the file unreadable by other programs like PAUP
without modification. Bug in versions 3.04-3.05.
- There were several instances where MacClade would give
incorrect warnings about conflicts between state symbols and
symbols used for missing data, gaps, and the matching character
symbol. Bug in versions 3.0-3.05.
- In some circumstances modal states were written incorrectly in
molecular sequence files. Bug in versions 3.0-3.05.
Bugs fixed in 3.07
- Some problems in importing and exporting PHYLIP files.
Bugs fixed in 3.08
- Some weight sets, type sets, and inclusion sets were
incorrectly written by previous versions.
- Crash if one deleted thousands of characters at once.
- PHYLIP files with taxon names right-justified were read
- The keyword "(STEPMATRIX)" was not recognized in a USERTYPE
definition in a NEXUS file
If you used Compress Characters, and a single cell was selected,
then the information would be incorrectly transported to another
- There were problems with some punctuation marks if used in
taxa, character, or state names.
- Couldn't read state names if the matrix was transposed and
MacClade was set to write files in the updated NEXUS format.
- Occasionally MacClade will give a warning, when going back to
the tree window, that MacClade had difficulty in restoring the
Evolve Segments. This can occur whether or not you have set the
evolve segments. If you see this behavior, please report it to
- MacClade 3 cannot read files that are on an MSDOS-formatted
"Suboptimalities" we haven't done anything about yet
- When an already-existing file is saved by MacClade, its
"Created" time (as seen in the Get Info window in the Finder) is
reset to be the same as its "Modified" time.
- When MacClade is open but no files are open, then
double-clicking on a MacClade file in the Finder of System 7
should cause MacClade to read in that file. This does not happen.
This is caused by a change in the file management software in
These are "anomalies" that are apparently not MacClade's
- Circle trees are not printed properly on some printers.
Apparently this is a bug in some printer drivers. We have noticed
this with Laserwriter driver 8.1.1; circle trees print fine with
Laserwriter driver 8.2.