Biology Reference
In-Depth Information
analysis methods, a particular tree is more likely to be correct (
Caterino et al.
2000
).
MrBayes
is available if you wish to carry out a Bayesian analysis of your data.
Phylogeny Inference Package
(
PHYLIP
) is available from Joseph Felsenstein,
Department of Genetics, University of Washington, Seattle, WA. It is a collec-
tion of
≈
30 independent programs implementing maximum likelihood, par-
simony, compatibility, distance, and invariant methods. Some of the programs
provide bootstrap methods for estimating confidence limits.
Phylogenetic
Analysis Using Parsimony
(
PAUP
) is available commercially (
http://paup.csit.fsu.
edu/downl.html
)
. PAUP performs parsimony analysis under a variety of mod-
els, and bootstrapping routines are available. Also available is BIOSYS-2, which
includes cluster analysis and distance Wagner routines for gene frequency
data.
Hennig86
is a small, fast, and effective program for parsimony analysis
under the Wagner and Fitch models.
MacClade
, written by
W. P. Maddison and
D. R. Maddison (2000)
, is useful in the analysis of character evolution and the
testing of phylogenetic hypotheses under the same parsimony models described
for PAUP plus additional ones.
Other software for phylogenetic analysis includes PALM, which assists in
choosing an appropriate substitution model (
Chen et al. 2009
). PAML 4 is a
package of programs for phylogenetic analyses using maximum likelihood
methods (
Yang 2007
), and Molecular Evolutionary Genetics Analysis (MEGA3)
facilitates analysis of DNA and protein sequence variation (
Kumar et al. 2004
).
Bayesian Evolutionary Analysis by Sampling Trees
(
BEAST
) (
Drummond and
Rambaut (2007)
and
Bayesian Analysis of Trees with Internal Node Generation
(
BATWING
) (
Wilson et al. 2003
) are available, as well as others.
Geneious, a DNA-sequence analysis software package for biologists, allows
DNA, RNA, and protein sequence alignment, assembly, and analysis. It integrates
bioinformatic and molecular biology tools with a user-friendly interface, allows
custom BLAST searches, sequence searches, and literature searches. Alignment
tools include ClustalW, MUSCLE, and MAFFT, translation and profile alignment,
and more. Geneious organizes data, stores data, and provides graphical outputs;
it can provide visualizations of three-dimensional structures, annotations, SNPs,
restriction sites, dot plots, and RNA secondary structures. It contains Mr. Bayes,
PAUP, Neighbor Joining, UPDMA, bootstrapping and consensus tree programs,
as well as primer-design programs (
www.geneious.com
). A simplified version is
available free (
www.geneious.com/basic
,
Kearse et al. 2012
).
Although there are concerns about the difficulty of calculating large phylog-
enies (
Degnan and Rosenberg 2009
),
Goloboff et al. (2009)
analyzed 13 genes
