Biology Reference
In-Depth Information
7 Materials
The following sections pertain to Apple computers running recent
versions of the Mac OS X operating system (including versions
10.4, 10.5, 10.6, and 10.7). For alternative operating systems and
hardware, please consult the relevant software documentation.
1. File format conversion software. SAT´ utilizes FASTA-formatted
sequence files and Newick-formatted tree files. Many software
packages and Web portals provide a format conversion capability.
For example, the European Molecular Biology Open Software
Suite (
http://emboss.sourceforge.net/
)
[
75
] contains a module
to convert sequence formats (see instructions for the seqret
command at
http://emboss.sourceforge.net/docs/themes/
SequenceFormats.html
)
. In addition, the savetrees command in
PAUP* [
76
] will output a tree in Newick format when the
“FORMAT
7.1
Software
PHYLIP” option is specified.
ware/SAT´/SAT´.html
.
We used version 2.2.5, although the
methodology in this chapter is compatible with any recent
version of the SAT´ software.
¼
1. We recommend using an Apple computer with a recent Intel
processor and at least 1 GB of available memory. Large-scale
analyses are primarily constrained by memory requirements
(
see Note 6
). Clock speed and related CPU features primarily
affect running time.
2. While the SAT´ installation requires less than 100 MB of disk
space, much more disk space is required for a large-scale analy-
sis, especially if the analysis runs for many iterations over a long
period of time (
see Note 7
).
7.2 Hardware
8 Methods
event of installation problems.
2. Open the downloaded package file and view its contents
(Fig.
1
).
3. Create a new folder for the new SAT
´
installation in a separate
location on the hard drive (
see Note 11
).
4. Drag and drop the package contents to the new folder.
5. In the new folder, double-click the SAT´ icon to start the SAT´
program.
8.1
Install Software
