#NEXUS BEGIN DATA; dimensions ntax=55 nchar=534; format missing=? symbols=”ABCDEFGHIKLMNPQRSTUVWXYZ” interleave datatype=DNA gap= -;

Change to as follows: #NEXUS BEGIN DATA; dimensions ntax=55 nchar=534; format datatype=dna interleave=yes gap=- missing=?;

then type mb -i *.nex

MrBayes > lset nst=6 rates=invgamma

Setting Nst to 6 Setting Rates to Invgamma Successfully [...]]]> Use clustalw to generate nexus format file

#NEXUS
BEGIN DATA;
dimensions ntax=55 nchar=534;
format missing=?
symbols=”ABCDEFGHIKLMNPQRSTUVWXYZ”
interleave datatype=DNA gap= -;

Change to as follows:
#NEXUS
BEGIN DATA;
dimensions ntax=55 nchar=534;
format datatype=dna interleave=yes gap=- missing=?;

then type mb -i *.nex

MrBayes > lset nst=6 rates=invgamma

Setting Nst to 6
Setting Rates to Invgamma
Successfully set likelihood model parameters

MrBayes > mcmc ngen=20000 samplefreq=100 printfreq=100 diagnfreq=1000

Setting number of generations to 20000
Setting sample frequency to 100
Setting print frequency to 100
Setting diagnosing frequency to 1000
Running Markov chain
MCMC stamp = 4956565474
Seed = 1367482907
Swapseed = 1367482907
Model settings:

………
MrBayes > sump
Type sump to summarize the parameter values using the same burn-in as
the diagnostics in the mcmc command. The program will output a table with
summaries of the samples of the substitution model parameters, including the
mean, mode, and 95 % credibility interval (region of Highest Posterior Density,
HPD) of each parameter.

MrBayes > sumt
The program will output a cladogram with the posterior
probabilities for each split and a phylogram with mean branch lengths. Both
trees will also be printed to a file that can be read by FigTree and other
tree-drawing programs, such as TreeView and Mesquite.

Note:
If the standard deviation of split frequencies is below 0.01 after 20,000
generations, stop the run by answering no when the program asks Continue the
analysis? (yes/no). Otherwise, keep adding generations until the value falls
below 0.01. If you are interested mainly in the well-supported parts of the tree, a
standard deviation below 0.05 may be adequate.

converting file formats
Having the proper data file format is essential as many programs can only input certain file types. The following are some of the input and output file formats for specific programs.

CLUSTAL file format:
Programs that input this file type: Clustal W/X
Programs that output this file type: Clustal W/X

FASTA file format:
Programs that input this file type: Clustal W/X, MAFFT
Programs that output this file type: Clustal W/X, MAFFT

NEXUS file format:
Programs that input this file type: BEAUti, GARLI, Modeltest, MrBayes, PAUP*
Programs that output this file type: Clustal W/X, PAUP*

PHYLIP file format:
Programs that input this file type: GARLI, LAMARC, Migrate-n, PAML, PHYLIP
Programs that output this file type: Clustal W/X, PAUP*, PHYLIP

PIR file format:
Programs that input this file type: Clustal W/X
Programs that output this file type: Clustal W/X

The commands referenced below are all part of special phylogenetic packages in R, not the basic R install. Be sure that you have installed and loaded the packages containing the commands referenced below before continuing. For example:

This loads the package ape and its required packages, gee, nlme and lattice, into your R [...]]]> http://www.r-phylo.org/wiki/HowTo/InputtingTrees

The commands referenced below are all part of special phylogenetic packages in R, not the basic R install. Be sure that you have installed and loaded the packages containing the commands referenced below before continuing. For example:

  library(ape)

This loads the package ape and its required packages, gee, nlme and lattice, into your R session.

How do I input a phylogeny into R?

Okay, so you’ve just completed a phylogenetic analysis or otherwise obtained a file containing a phylogeny, and you’d like to use that phylogeny as a framework for comparative analysis in R. R packages for phylogenetics may differ in how they represent phylogenies. The most commonly used is the “phylo” (more specifically, objects of class “phylo”). Luckily, converting your phylogeny to “phylo” representation is easy.

The package APE can read phylogenies in either Newick or NEXUS format using the read.tree and read.nexus commands, respectively. (Note: we assume you have already placed these input trees in your working directory, see the basics)

  MyTree <- read.tree("MyNewickTreefile.tre")
  MyTree <- read.nexus("MyNexusTreefile.nex")

Either of these commands will create an identical object called “MyTree” in R containing your phylogeny. This object is in “phylo” representation and it can be input to various other functions in R.

If you have the sample Geospiza phylogeny saved to your working directory, this command will load it into memory.

  geotree <- read.nexus("geospiza.nex")

Note that when you construct the original Newick or NEXUS files you should avoid enclosing your taxon names within quotes or using blank space within taxon names. A taxon named Genus_species will work fine, one named “Genus species” will not. R and APE support the use of translation tables for taxon names in NEXUS format, but not in Newick format.

How do I export a phylogeny out of R?

APE can export phylogenies in phylo representation into either Newick or Nexus format using the write.tree and write.nexus commands, respectively.

  write.tree(MyTree, file="MyNewickTreefile.tre")
  write.nexus(MyTree, file="MyNexusTreefile.nex")

What if I’m working with multiple trees?

No problem! If the Newick or NEXUS file that you read into R contains multiple trees, an object called a list will be created. Each element of the list will be one individual tree from the original datafile.

You can also write multiple trees to a single file from R. If the trees are already in a list (perhaps one called MyTrees), the syntax is the same as above.

  write.nexus(MyTrees, file="MyNexusTreefile.nex")

If trees are not in a list but exist instead as separate objects, you can type them as sequential arguments in write.nexus.

  write.nexus(MyTree1, MyTree2, MyTree3, file="MyNexusTreefile.nex")

Write.tree currently accepts a only single tree as input.

However, be aware that many functions in R are designed to accept only a single tree as input, not a a list of trees. You can apply a single function to all the elements of a list sequentially using the lapply and sapply commands. For more information on the usage of lapply and sapply, type either of the following into the R command line.

  help(lapply)
  help(sapply)

• Also see Rich Glor’s page from the Bodega Applied Phylogenetics Workshop

Credit: Most of the information on this page is based on the book Analysis of Phylogenetics and Evolution with R (Paradis, 2006).