New Features and History of Changes
Here are some of the more notable new features and bug fixes
since version 1.0.
- 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
- 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
- fixed tree printing bug by which node numbers and branch lengths
- 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