REvolver: Modeling sequence evolution under domain constraints
Introduction:
REvolver is a program to simulate protein sequence evolution. REvolver automatically integrates domain information described by a profile Hidden Markov Model (pHMM) into the
simulation. In the simulation of protein evolution it often had been assumed that sites
evolve identically and independently from each other. This simplification is necessary since
information concerning site specific evolution is frequently unavailable. However, homologous sequences and domains have been collected, aligned, and pHMMs built. The pHMM
describes the variability and shared characteristics of sequences that share a common ancestor. Here we do have knowledge about what sites are conserved, at what positions in
the sequences insertions are more likely, or what sites can be deleted. Pfam (Finn et al.,
2010) and SMART (Letunic, Doerks and Bork, 2009) are examples for databases providing
such data. REvolver is the first method, for simulating protein sequence evolution that
integrates this pre-existing information about evolution in an automatic fashion.
REvolver
Methods:
The method is described in the following article:
- Tina Koestler, Arndt von Haeseler, and Ingo Ebersberger
(2012) REvolver: Modeling sequence evolution under domain constraints.
Mol Biol Evol (DOI: 10.1093/molbev/mss078, PMID: 2383532), accepted.
External programs required:
REvolver is written in java, thus you need to have java 6 installed. The HMMER3 software package (
HMMER3) has to be installed. Please note, hmmscan need to be run with the option
--notextw.
Please download any pHMM database you want to use for REvolver simulations (e.g.
Pfam, or
SMART).
Version history:
- August 2011: The first version of REvolver was released.
- February 2012: Manuscript was accepted for publication in MBE
Note:
Please read the manual carefully if you try our program the first time. If you encounter bugs, please report to tina.koestler(AT)univie.ac.at.
The source code is available upon request.
