Features added to MacClade 4 since version 4.0

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

Here is a list of features added to MacClade since version 4.0 was released. The names of those who suggested each feature (if someone other than DRM and WPM) are given in parentheses after the feature. There are also additional minor features added.

New features included in 4.01

• Ability to define and manipulate character groups, and to save the assignment of characters to groups as a character partition. This is mainly of use for interaction with other programs such as PAUP, but you can also have MacClade color characters by the group to which they belong.
• The Calculate Codon Positions dialog box now has an option to ask MacClade to try three possible reading frames and choose the one which minimizes the number of implied stop codons.
• MacClade can now automatically shift a sequence through the reading frame to minimize the number of stop codons.
• "Last Tool" menu item to allow you to quickly toggle between two tools in the data editor or tree window. (Steve Haddock and DRM.)
• The Select To End tool in the data editor now has an option to avoid selecting leading/terminal gaps. (Steve Haddock.)
• The "Collapse Gaps" tool in the data editor now has an option to move only one leading base.
• The data editor has the option to flash sequences that are reverse complements to a selected block, using rRNA pairing rules (i.e., A or G are considered complementary to T/U). It allows up to a specified number of mismatches. Not available in the classroom version.
• The Find facility in the data editor now allows up to a specified number of mismatches.
• The ability to color data by having the text of a cell colored rather than its background. (Bengt Oxelman.)
• Exporting sequences in MALIGN format. (Kip Will.)

New features included in 4.02

• Increase in the maximum number of allowed characters from 16,000 to 32,000.

New features included in 4.04

• Native version for MacOS X
• Speak Matrix can be restricted to only speak the currently selected block.
• In the MacOS X and normal PowerPC versions of MacClade any type of file can be opened, even if it is not marked as a text file. (Of course, the file must be a text file in a readable format.)

New features included in 4.05

• The ability to find partial triplets in coding regions.
• The "Shift Selected to Minimize Stop Codons" feature, in which MacClade will shift protein-coding DNA sequences so that each sequence has fewer stop codons, and "Import NBRF Protein Alignment", with which you can realign DNA sequences to match a protein alignment, are not new, but are no longer hidden features.

New features included in 4.07

• Automatic shifting of sequences so that a region in them lines up with a selected region in another sequence. This greatly speeds up manual alignment.
• The ability to export FASTA files.
• Copying a block of matrix cells to the clipboard.
• Inclusion of a prebuilt set of nucleotide colors to match those used in Sequencher.
• Dimming of lower-case nucleotides in the data editor.
• Showing percentage of lower-case nucleotides in the Taxon List window.

New features included in 4.08

• Showing number of uncertainties or polymorphisms in the Taxon List window.