indel-Seq-Genv2.0
 

Author:Cory Strope cstrope AT cse DOT unl DOT edu

 
indel-Seq-Gen allows the user to simulate multiple subsequences according to different evolutionary parameters, allowing for the simulation of realistic families of protein sequences. indel-Seq-Gen records all evolutionary events and outputs the ``true'' multiple alignment of the sequences, and can generate a larger simulated sequence space by allowing the use of multiple related root sequences. indel-Seq-Gen can be used to test the accuracy of multiple alignment methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein superfamily classification methods. indel-Seq-Gen is built on top of Seq-Gen [3].
 

indel-Seq-Gen (v. 2.0) Downloadable files:

• indel-Seq-Genv2.0 Source

Obselete versions:

• Version 1.0.3
• Version 1.0.2
• Version 1.0.1
• Version 1.0

To extract .tar.gz files, type:

• gunzip [filename].tar.gz
• tar -xvf [filename].tar.

For a manual of indel-Seq-Gen v2.0 commands, click here.

v1.0.3

indel-Seq-Gen has been tested on RedHat Linux, SuSE Linux, IRIX, and MacOS X (versions 10.3.9, 10.2.8, and 10.4.7). In addition to the gcc compiler (if the provided executables do not run on your system), indel-Seq-Gen requires PERL. We have not tested indel-Seq-Gen on Windows environment. The indel-Seq-Gen ZIP archive provided above does not include executables for Windows.

Version Information

v2.0

indel-Seq-Gen version 2.0 [2] (Open Access) includes the following functionality upgrades:

• Includes protein, coding DNA, and non-coding DNA simulation,
• Incorporates PROSITE-like regular expressions for motif conservation,
• Allows the user to impose minimum and maximum lengths on subsequences (e.g., GPCR transmembrane subsequence can be a minimum of 17 and a maximum of 24 amino acids),
• Changed continuous simulation by breaking up branch lengths into small, discrete values.
• Logs insertion and deletion events, outputting
  1. Type of event,
  2. branch of occurrence,
  3. length of event,
  4. relative time of occurrence, and
  5. position of the inserted characters (for insertions) or gaps (for deletion) in the true multiple sequence alignment.
• Introduced a novel representation of event probability (insertions, deletions and substitutions) for a sequence that is constrained, and
• Fixed a flaw in the modeling of indels (see [2] for details).

The Perl script from iSGv1.0 has been converted into ANSI C++, and iSGv2.0 is now packaged using GNU autotools for compatibility.

1.0.3

Fixed the problem of no indels occurring with the Chang and Benner model of indel evolution.

1.0.2

Fixed ancestral sequence option (indel-Seq-Gen option ``-w a''). NOTE: Unlike seq-gen, indel-Seq-Gen will allow you to use the ancestral sequence output option for multi-partition simulation runs. However, all partitions MUST have the same branching pattern for the output ancestral sequences to be meaningful. Ancestral sequences are also included in the true multiple alignment.

1.0.1

indel-Seq-Gen script finds PERL environment, makes portable calls to seq-gen-i. Fixed bug related to the phylip output format.

Bibliography

1

Strope, C.L., Scott, S.D., and Moriyama, E.N. 2007. indel-Seq-Gen: A new protein family simulator incorporating domains, motifs, and indels. Mol. Biol. Evol 24: 640-649.

2

Strope, C.L., Abel, K., Scott, S.D., and Moriyama, E.N. 2009. Biological sequence simulation for complex evolutionary hypotheses with indel-Seq-Gen version 2. Mol. Biol. Evol doi:0.1093/molbev/msp174.

3

Rambaut, A. and Grassly,N. 1997. Seq-Gen: an application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees. CABIOS 13:235-238.