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 -