# Differences Between Version 2 and Version 3

### From MbWiki

We have discontinued the development of version 2 of MrBayes and recommend all users to switch over to version 3. With the release of version 3.1, virtually all models implemented in version 2 are available in version 3 (plus many more). The only exception is the time-irreversible model of nucleotide evolution, which is still not implemented in version 3. If you are interested in seeing this model reappear, let us know.

An important difference between versions 2 and 3 is found in the way models are defined. MrBayes 3 by default estimates most parameters, there is no need to specify `estimate` for any parameter. Some things that were previously set using `lset` are now set using `prset`. This is true for the amino acid model and for the site specific rates (see section 4 of this manual for more information on the site specific rate model in version 3). Thus, site-specifc rates, for instance, can no longer be invoked using `rates=sitespec`.

In more detail, the changes are as follows, with emphasis on the features in version 2 that are implemented differently in version 3 (commands and options in version 2 listed alphabetically):

**calibration**. Calibration of clock and relaxed-clock trees is not (yet) implemented in MrBayes 3.

**constraint**. The format of the constraint now includes a probability value (`constraint <name> <probability> = <list_of_taxa>`). The probability value is ignored by version 3.1 of the program but it must be included in the constraint definition. The probability value will be used by future versions of the program.

**lset aamodel**. The amino-acid model is now `set using prset aamodelpr`.

**lset ancfile**. Ancestral states are now written to the `.p` file(s).

**lset basefreq**. Whether this parameters is estimated or fixed to a particular value in version 3 is controlled by setting the prior with `prset statefreqpr`. By default, all parameters are estimated. There is no `basefreq` option in the `lset` command of version 3 of MrBayes.

**lset clock**. Whether the tree is a clock or a non-clock tree is now set using `prset brlenspr`.

**lset enforcecal**. Calibrations are not implemented (yet) in MrBayes 3.

**lset enforcecodon**. The type of nucleotide model is now set using `lset nucmodel=4by4/doublet/codon`.

**lset enforcecon**. Now set using `prset topologypr = constraints (<list_of_constraints>)`.

**lset inferanc**. Now set using `report ancstates`.

**lset inferpossel**. Now set using `report possel<tt>.
`

` lset inferrates. This is now set with <tt>report siterates`.

**lset ncat** (number of categories used to approximate the gamma distribution of site rates). Now set using `lset ngammacat` to distinguish it from `nbetacat` (the number of categories used to approximate the beta distribution of rate / stationary state asymmetry across sites in the standard model).

**lset nonrevmat**. Time-irreversible models are not implemented in MrBayes 3.

**lset omega**. Whether this parameters is estimated or fixed to a particular value in version 3 is controlled by setting the prior with `prset omegapr`. By default, all parameters are estimated. There is no `omega` option in the `lset` command of version 3 of MrBayes.

**lset rates**. The site specific rate models (`sitespec`, `ssgamma`, `ssadgamma`) are now set using the more general partitioning model. See section 3 of this manual as well as the discussion of partition models in section 4.

**lset revmat**. Whether this parameters is estimated or fixed to a particular value in version 3 is controlled by setting the prior with `prset revmatpr`. By default, all parameters are estimated. There is no `revmat` option in the `lset` command of version 3 of MrBayes.

**lset seqerror**. The model of sequencing error is no longer implemented in MrBayes 3. The model typically results in small corrections in partition support values but it conflicts with important algorithmic short-cuts implemented in version 3.

**lset shape**. Whether this parameters is estimated or fixed to a particular value in version 3 is controlled by setting the prior with `prset shapepr`. By default, all parameters are estimated. There is no shape option in the `lset` command of version 3 of MrBayes.

**lset sitepartition**. The partition of sites is now set using `set partition`.

**lset tratio**. Whether this parameters is estimated or fixed to a particular value in version 3 is controlled by setting the prior with `prset tratiopr`. By default, all parameters are estimated. There is no `tratio` option in the `lset` command of version 3 of MrBayes.

**prset basefreqpr**. Now set using `prset statefreqpr`.

**prset brlenpr**. Now set using `prset brlenspr`. The options are now more complicated as well, since the prior includes information both about the general type of the branch lengths (clock, non-clock) and the specific shape of the prior (for example, uniform or exponential).

**prset siteratepr**. Now set using `prset ratepr`. The options are fixed or variable (Dirichlet). The parameters of the Dirichlet can be set to reflect various types of prior information concerning the site rates.

**prset qmatpr**. Now set using `prset revmatpr` and `prset aarevmatpr` for nucleotide and amino-acid substitution rates, respectively.

**set**. This command only controlled the `autoclose` option in MrBayes 2. In version 3 it controls a number of different things, including the currently selected partition.

**shownodes**. This command is no longer included in MrBayes 3. Use `showtree` to display the user tree.