ben stöver ws 2012/2013 ancestral state reconstruction molecular phylogenetics – exercise
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![Page 1: Ben Stöver WS 2012/2013 Ancestral state reconstruction Molecular Phylogenetics – exercise](https://reader037.vdocuments.site/reader037/viewer/2022110103/5697bfcf1a28abf838ca9cdb/html5/thumbnails/1.jpg)
Ben Stöver WS 2012/2013
Ancestral state reconstruction
Molecular Phylogenetics – exercise
![Page 2: Ben Stöver WS 2012/2013 Ancestral state reconstruction Molecular Phylogenetics – exercise](https://reader037.vdocuments.site/reader037/viewer/2022110103/5697bfcf1a28abf838ca9cdb/html5/thumbnails/2.jpg)
Ben Stöver
Ancestal state reconstruction with BayesTraits
Fortgeschrittenenmodul Molecular Phylogenetics
Winter term 2012/2013
13.02.2012
1 Ancestral state reconstruction1. Ancestral state reconstruction 2
• Reconstructing character states of acenstral nodes
• Tree topology is given• Terminal character states are given
• Top left charts: Female gametangia (green: ventral, red: marginal, blue: central)
• Top right charts: Mycothallus (green: parenchymal, red: epidermal, blue: none)
• Bottom charts: Scales (yellow: small, green: broad marginal, red: lateral on margin, blue: broad central)
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Ben Stöver
Ancestal state reconstruction with BayesTraits
Fortgeschrittenenmodul Molecular Phylogenetics
Winter term 2012/2013
13.02.2012
2 Mesquite2. Mesquite 3
• Modular software system• Ancestral state reconstruction
with parsimony or likelihood• (No Bayesian methods
available)• Many other features• Distributed under GPL
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Ben Stöver
Ancestal state reconstruction with BayesTraits
Fortgeschrittenenmodul Molecular Phylogenetics
Winter term 2012/2013
13.02.2012
3.1 BayesTraits – overview3. BayesTraits 4
Parts of the software:
• BayesMultistate• Reconstructs characters with multiple (more than two) states
• BayesDiscrete• Analyze correlated evolution between pairs of discrete binary traits
• BayesContinues• Analysis of the evolution of continuously varying traits (e.g. length of an
organ)
• BayesTraits is a command line based software (like PAUP* and MrBayes)
• Performs maximum likelihood or Bayesian reconstruction.
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Ben Stöver
Ancestal state reconstruction with BayesTraits
Fortgeschrittenenmodul Molecular Phylogenetics
Winter term 2012/2013
13.02.2012
3.2 Starting BayesTraits
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• BayesTraits takes two command line parameters.• BayesTraits.exe <TreeFile> <DataFile>
• The tree file may also contain a tree distribution (e.g. from MrBayes)• The data file contains a table specifying the terminal character states.
• In the start menu the part of the program to be used must be selected
• The method is selectes afterwards
3. BayesTraits
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Ben Stöver
Ancestal state reconstruction with BayesTraits
Fortgeschrittenenmodul Molecular Phylogenetics
Winter term 2012/2013
13.02.2012
3.3 BayesTraits commands
6
• sample <n>: Sets the sample frequency.• iterations <n>: Specifies the number of generations for the MCMC-
algorithm.• burnin <n>: Sets the generation count of the burin.• revjumphp: Specifies the distribution of prior probabilities (only
for MCMC)• AddNode: Defines an exact node to be reconstructed.
(e.g.: AddNode Node01 51 52 50 49 47 48)• AddMRCA: Defines a node to be reconstructed that is the
most recent common ancestor of the specified taxa (but might also be the acestor of additional taxa.)
• fossil: Specifies an ancestral state already known. (e.g.: fossil Node1 0 51 52 50 49 47 48 sets
the state of Node1=0)• info: Prints out information of the current settings.• run: Starts the analysis.
3. BayesTraits
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Ben Stöver
Ancestal state reconstruction with BayesTraits
Fortgeschrittenenmodul Molecular Phylogenetics
Winter term 2012/2013
13.02.2012
3.4 Output of BayesTraits
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• BayesTraits generates a text file containing a table with the posterior probabilities of the samples (or likelihoods).
• Each line describes one sample the MCMC algorithm took. • (For ML with a single tree, there will only be one line.)• There is one column for each state of each character that was
reconstructed.
3. BayesTraits