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Seq-Gen was developed to be a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process.
A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.
Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.
Seq-Gen is a command-line controlled program written in ANSI C. It should be easily compiled and run on any UNIX system or workstation. This paper describes the use of Seq-Gen on a UNIX machine. The application requires an amount of memory proportional to the size of each simulated sequence data set.
Running Seq-Gen
To run Seq-Gen you type:
seq-gen [parameters] [sequences]
where [parameters] are the parameters for the program (described below), [trees] is the tree file and [sequences] is the name of the file that will contain the simulated sequences. The tree file must contain one or more trees in PHYLIP format.
The sequences produced by Seq-Gen are written to the standard output (and can thus redirected to the output file using > [filename]). Other information and results are written to the standard error and thus will appear on the screen.

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In Seq-Gen the tree is specified using the DOT language syntax. The DOT language is based on command-line-editing techniques used in UNIX text editors. It is a rather complex language but for an introduction to the use of the DOT language see the Seq-Gen manual.
A sample tree is shown below:
Tree #1:
name (stem) n1 n2 #trees
1
2
3
4
5
6
7
8
9
10
11
.
.
.
1 2 3 4 5 6 7 8 9 10 11
.
.
.
The names of the branches of the tree are written under the #trees at the start of each line. The branches represent the tips of the tree. A branch has two nodes, one for each parent of the branch, and these nodes are indicated by n1 and n2. The numbers of the nodes are the order in which the nodes appear on each branch (so a node number of 2 indicates that node 2 was the parent of branch 1).
The tree also has an optional number of mid-branches, defined by the colon. The three mid-branches of the above example are shown in bold. This number indicates the length of the mid-branch relative to the length of the tree (so the tree in the example has three mid-branches).
Any number of nodes may be connected to a node by a name and then separated from the node by a comma. Thus there can be a large number of nodes in the tree.
There is also the option of putting the tip of the tree on the root of the tree, by replacing the #trees at the start of each line with “root”. This option may be used to simplify the description of the root of the tree (i.e. to avoid the need for an explicit “root” label).
Any number of sequences may be associated with each node in the tree. The sequence associated with a node is given by the second column of the node. Thus, for the tree shown above, sequence 1 is associated with node 1, sequence 2 is associated with node 2, etc.
Each node in the tree can have any number of sequences associated with it.
In addition to the tree parameters, there are several other parameters that can be specified for Seq-Gen. The first is the minimum and maximum number of sequences that will be produced by the program. These values must be

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Macro which will enable or disable the use of a user-specified MACRO (command) to enter data into the simulated data set. In addition to the MACRO the user is also given a number, the argument, on which to call the command. The MACRO should set the environment variable “SEQGEN_MACRO” to the name of the command that will be entered.
Generate Data:
This generates the data for the simulated sequences. The format of the input data file and the defaults of the simulated sequences are shown. Two separate data files (for nucleotide and amino acid sequences) are generated with the number of sequences in the data file being the sum of the input number of sequences and the default number of replicate sequences. Thus if 10 nucleotide sequences and a default of 10 replicate sequences are specified the output will have 21 sequences.
Computational Details:
All simulated sequences are coded on the assumption that the characters in the simulated sequences are evenly spaced apart. A different set of arguments controls the spacing and code of the simulated sequences. It is assumed that each state in the sequence is evenly spaced apart, but the distances between each state can be specified by giving the first and last positions of each state. As an example the number of bases in a simulated sequence can be specified, with each base being given at a particular distance from the previous base (for nucleotide sequences). A single base will be included for each state in the sequence. To illustrate, if the sequence of bases in a 20-state sequence is [b1 b2 b3 b4 b5 b6 b7 b8 b9 b10 b11 b12 b13 b14 b15 b16 b17 b18 b19 b20] the first base is in position 9. Thus the defaults for the program are:
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Parameters for Seq-Gen are:
* Prints a summary of the output data set.
* Prints the phylogeny describing the input trees.
* Allows the substitution process to be non-stationary.
* Allows the substitution process to have different rates at different sites.
* Generates the complete history of the sequences (as opposed to just the sampled portions).
* The program is designed to be fast and generally runs on any UNIX system (including Macs) or workstation with an average of 64 MB of RAM.
* The program is written in ANSI C and runs on any UNIX system or workstation that has gcc installed.
* Seq-Gen is based on a version of the HKY model developed by Felsenstein (1981).
This model is very commonly used and described in much detail in graduate texts and in papers such as by Yang (1994). This paper is a very nice description of some of the concepts and terms used in Seq-Gen. You can see a list of references at the end of this paper.
The GTR model is also implemented in Seq-Gen. However, while this model has certain advantages it is not as widely used as the HKY model. This is because it allows site-specific rate heterogeneity, which makes it much harder to infer the parameters of the model (Rannala and Yang, 1996). This is not always a problem, however.
In order to allow for differences in base composition and to incorporate some measure of rate heterogeneity, Seq-Gen uses the standard HKY model, with the difference that it does not have a stationary nucleotide frequencies.
Seq-Gen will generate data sets that approximate those generated under the HKY model (which is not exactly equivalent to the HKY model) but allows for deviations from stationarity.
If the SEQGENDIST option is given the program will simulate the evolution of the sequences along the tree starting from a randomly chosen node in the tree. The program will simulate 1000 or 5000 replicate data sets (using the FAST option).
If the TIMES and the STATES options are given the program will simulate the evolution of the sequences for a specified number of time steps.
If the HISTORY option is given the program will produce the full history of the sequences, that is the complete phylogenetic tree that is used to make the evolution simulation.
If the LEN option is given the program will set the length of the sequences (that is

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Seq-Gen simulates the evolution of DNA or amino acid sequences under one of several commonly used evolutionary models, which include the general reversible model, the general site-heterogeneous model, and the invariable site model. When simulating the evolution of DNA sequences, the model is specified by the nucleotide substitution matrix. The most common matrices are Dayhoff and Kimura. The amino acid substitution matrices used are the standard model and the general model.

The currently implemented options are:
-v, –verbose: increase the amount of output on the screen.
-i, –ignore-pair: ignore insertions and deletions in the model.
-n, –name: the branch length will be given a name.
-o, –outdir: The sequence files are saved to this directory.
-r, –replicates: The number of sequence replicates (trees) is given as this number.
-u, –unifreq: The base frequencies and rates of the model are given as this number.
-m, –maximum: The maximum number of bases or amino acids the program will accept is given as this number.

Seq-Gen was written with UNIX in mind, and therefore the number of sequences and trees are specified on the command line. Any number of sequences may be specified. As the trees are read in they are saved to disk. Thus the -r parameter is ignored, as there is no need to use that parameter when running Seq-Gen.

Example:

Seq-Gen can be used to produce a number of simulated sequence data sets. The simplest application of the program is to produce a large number of replicate sequence data sets for a given tree (assuming that the tree has been previously read in).

Syntax:

seq-gen [parameters] [sequences]

where [parameters] are the parameters for the program (described below), [sequences] is the name of the file that will contain the simulated sequences. The tree file must contain one or more trees in PHYLIP format.

The sequences produced by Seq-Gen are written to the standard output (and can thus redirected to the output file using > [filename]). Other information and results are written to the standard error and thus will appear on the screen.

A detailed description of Seq-Gen, along with examples, may be found on the Seq-Gen page.

Details:

The output is specified by a tree file in PHYLIP format. Seq-Gen will read in multiple trees in the same file. The program will simulate the evolution of a sequence over the tree(s) read.

The parameters are described below.

Parameters:

The parameters

System Requirements:

Windows 8.1, Windows 7, Windows Vista, Windows XP.
3.8 GHZ or faster PC.
1 GB RAM.
500 MB Disk space.
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