Biology Reference
In-Depth Information
subsets (carefully selected from the taxon set), and combines these
smaller trees into a tree on the full set of taxa using SuperFine
[
77
-
79
]. By combining this divide-and-conquer strategy with iter-
ation, it quickly produces highly accurate trees. Truly alignment-
free estimation has also been considered [
80
,
81
], with some meth-
ods have strong theoretical guarantees [
82
]. Certainly the benefits
of not requiring a full multiple sequence alignment are significant,
especially in terms of running time. Ongoing research will show
whether methods that do not require full sequence alignments are
able to produce trees of comparable accuracy to the best of the tree
estimation methods that do (at some point) estimate an alignment
on the entire dataset.
This tutorial is limited to the GUI usage of SAT´; readers
interested in using the command line version are directed to the
online tutorial [
83
]. Datasets and software to study alignment
and phylogeny estimation methods are available through the
SAT´ group Webpages at UT-Austin [
84
]. For additional discus-
sion on methods for phylogenetic analysis, including data selection,
see [
85
,
86
].
10 Notes
1. This chapter is adapted from part of the SAT´ tutorial materials
available at
http://phylo.bio.ku.edu/software/sate/sate_
2. A SAT´ user group provides announcements about SAT´ devel-
opment, user support, and a general discussion area for all
matters related to SAT´. See the “SAT´ User Group” section
3. SAT´ is under active development. See the SAT´ Webpage
at UT-Austin,
http://www.cs.utexas.edu/~phylo/software/
sate/
for discussion about new and experimental features.
4. Do not set the “CPU(s) Available” setting to greater than the
number of physical computing cores available on the computer.
Doing so can overload computational resources and slow down
the SAT´ analysis. To find out the number of computing cores
on your computer, open the System Information utility in OS
X (Apple icon in top left
About This Mac
More Info
>
System Report). The main screen of this utility will show
the number of cores (“Total Number of Cores” field in the
“Hardware Overview” panel).
5. MSA and biomolecular sequence files can require a significant
amount of disk space. Since intermediate results—including
intermediate MSA file—are stored during a SAT´ analysis,
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