AutoDecay 5简要说明
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AutoDecay 5.0 README for UNIX, Linux, BSD, Mac OS X, etc.
This version of AutoDecay is written in Perl () an open source
("free") programming language.
Versions:
1.0 First Hypercard Stack for Apple Macintosh
2.0 Rewritten Hypercard Stack
3.0 C-version for Apple Macintosh written with N. WikstrC6m
4.0 Amended Hypercard stack. Standalone versions distributed
5.0 Perl version, Aug. 2001
It may be possible to obtain various previous versions. The latest versions may
be found at: http://www.bergianska.se/personal/TorstenE/
From August 2001 only the Perl version is maintained.
Perl runs on most platforms including flavours of UNIX (Linux, BSD
including Mac OS X and others), Windows and Mac OS Classic (MacPerl is used for
system versions before 10). In this way AutoDecay has now become much more
accessible. If you don't have Perl, see for info on how to
obtain it.
Version 5.0 differs from previous versions of AutoDecay:
* Designed to use PAUP* 4.0. Older versions of PAUP may not work.
* Invoked from the command line.
* Minor changes in internal file format (simple fix can be applied to old files).
* Uses shorthand version of constraint trees.
* Defaults for PAUP* runs are read from settings file.
* Any of the tree, adc or log files can be input for the extraction
* No multiple command files. (Ask me if you really need it)
* No scaling of weights
INSTALL
* Download the file autodecay-.tar.gz to where you want AutoDecay.
* Gunzip and Extract the files. A directory 'autodecay' will be created.
* The following files are included:
Folder UNIX
AD - The AutoDecay program
AD.def - Settings file containing defaults
HelpText - Info on how to run AutoDecay
README - This file
Folder MacClassic
AD - The AutoDecay program
AD.def - Settings file containing defaults 2
HelpText - Info on how to run AutoDecay
README-Mac - Apple Macintosh readme
Folder WinDOS
AD - The AutoDecay program
AD.def - Settings file containing defaults
HelpText - Info on how to run AutoDecay
README-WinDOS - Microsoft readme
The only real difference (except for the README files) is that the line endings
are adjusted appropriately. Move the set of files which is appropriate for your
system, to a convenient location.
* Check that AD is executable by you
* Adjust $PATH if need be or copy AD to a directory which is in your path.
* If your perl executables don't reside in /usr/bin you'll have to modify
the first line of AutoDecay accordingly.
* Read the HelpText.
I've been told by my colleagues that there may be others out there who
might want to use my auto decay tool. Here is a short description:
Background
In wanting to assess the node support in phylogenetic hypotheses, K. Bremer
[The limits of amino acid sequence data in Angiosperm phylogenetic
reconstruction. Evolution. 42: 795-803 (1988)] estimated how much longer a
tree had to be before a particular node was lost. He did this by saving all
shortest trees, the ones one step longer, and then computing a strict
consensus tree. Then adding all cladograms two steps longer and
"consensing" all together, noting which nodes collapsed at each step - and
so on. The difference in length between the shortest three(s) and the
tree(s) collapsing a certain node has then been used as an index of support
for that node ("Decay index").
There is a problem with this approach: Trying to save all trees, say, 10
steps longer than the shortest ones might be impossible for practical
purposes due to limited time and computer memory. A solution was
incorporated (although, it seems, not generally known) in PAUP [Swofford,
D. L. PAUP: Phylogenetic Analysis Using Parsimony (Computer program).
Smithsonian Institution, Washington. (1993)]. Swofford applied reverse
constraints which accomplished the same function. However, and here is why
I actually made this tool, it is kind of tedious to make the constraint
trees needed to test all nodes in a tree.
What Auto Decay does 3
It reads a nexus file including a trees block with at least one tree. It
decomposes this tree and creates constraint trees for every node. A PAUP
command file is then made with all necessary commands to automatically run
a reverse constraint analysis (batch file in PAUP) for every node in the
tree. It then reads the PAUP log file and computes node support indices for
all nodes.
What Auto Decay is
It is a Hypercard stack which means that an Apple Macintosh is needed. You
will need Hypercard 2.0 or later and HyperCard Player is sufficient. You
also need PAUP 3.1.1. It may be possible to run on older versions of PAUP -