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http://ib.berkeley.edu/courses/ib200a/labs/ib200a_lab10_bootstrap_jackknife_bremer.pdf
You may remember finding Bremer support from the lab on “Advanced PAUP,” but I’ll go over it again anyway. First, you’ll need to switch to a new data file—the primates.nex file isn’t a very good example for Bremer support because everything has a really high decay index. 12.
https://www.geol.umd.edu/~tholtz/G331/lectures/cladistics5.pdf
for morphological data: Bremer support and the Bootstrap. Bremer support is by far the most useful for the amount of data we use as palaeontologists (we rarely have more 100 characters). Bremer support is named after the Swedish botanist Kore Bremer, who devised the method, but it is also known as the “Decay Index”, for reasons that will
https://en.wikipedia.org/wiki/Maximum_parsimony_(phylogenetics)
Maximum parsimony is an intuitive and simple criterion, and it is popular for this reason. ... as are the bootstrap and jackknife procedures described above. Bremer support ... Double-decay analysis is a decay counterpart to reduced consensus that evaluates the decay index for all possible subtree relationships (n-taxon statements) ...
http://www.mobot.org/plantscience/ResBot/Repr/Zander-Phyloinformatics2004.pdf
The Decay Index (also known as Bremer Support) (Bremer 1988, 1994; DeBry 2001; Giribet 2003; Morgan 1997) is another measure of clade reliability commonly defined as the number of steps needed to "relax" parsimony until a given branch arrangement collapses …
https://ib200lab.files.wordpress.com/2014/01/ib200_lab06_support_measures.pdf
Exercise 4: Estimate Support by Bremer Support/Decay Index For those that eschew a statistical view point (or who like to use a few different frameworks), a good alternative is to determine whether a group of interest occurs in other trees that are almost equally short. Another way to this about this is to consider that with every tree
http://www.iab.uaf.edu/people/derek_sikes/Biol615/handouts/BIO615-25.pdf
1. Consistency Index 2. g1 statistic, PTP - test 3. Consensus trees 4. Decay index (Bremer Support) 5. Bootstrapping / Jackknifing 6. Statistical hypothesis testing (frequentist) 7. Posterior probability (see lecture on Bayesian) Confidence - Assessment of the Strength of the Phylogenetic Signal - …
http://ib.berkeley.edu/courses/ib200a/ib200a_sp2008/Lab12_Support.pdf
You may remember finding Bremer support from the lab on “Advanced PAUP,” but I’ll go over it again anyway. First, you’ll need to switch to a new data file—the primates.nex file isn’t a very good example for Bremer support because everything has a really high decay index. 11.
http://evolution.genetics.washington.edu/phylip/software.pars.html
Torsten Eriksson of the Bergius Botanical Garden, Stockholm, Sweden (torsten (at) bergianska.se) has written a program, AutoDecay which generates Decay Indices from an existing PAUP* 4.0 treefile. It is intended to simplify the the task of creating reverse constraint trees in PAUP* 4.0 and subsequent generation of Bremer support values.
https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-5-58
Oct 29, 2005 · For parsimony analyses, the most common way to estimate confidence is by resampling plans (nonparametric bootstrap, jackknife), and Bremer support (Decay indices). The recent literature reveals that parameter settings that are quite commonly employed are not those that are recommended by theoretical considerations and by previous empirical studies. The optimal search strategy to be …Cited by: 138
https://www.researchgate.net/publication/11261747_Improving_Interpretation_of_the_Decay_Index_for_DNA_Sequence_Data
Improving Interpretation of the Decay Index for DNA Sequence Data. ... total decay index and partitioned Bremer support (PBS) values were determined using TreeRot 3.0 (Sorenson & Franzosa, 2007 ...
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