ReEVOLVER 1.0

A tool to detect functional lineage-specific genes by evolutionary simulations

Introduction

Input files

Running

Output files

References

Download

Introduction

The ReEVOLVER 1.0 software implements an approach that can be used to support the functionality of recent duplicate genes using evolutionary simulations. By repeatedly simulating the evolution of a putative gene under neutrality, our method estimates the probability that its open reading frame has been selectively preserved during its evolutionary history and is therefore likely to be functional. In parallel, our method tests whether the accumulation of nonsynonymous substitutions is consistent with neutrality or selective constraint. The method is described in Dupanloup and Kaessmann (submitted).

Linux, Mac (OS X 10.4), and Windows versions of the ReEVOLVER 1.0 software are available.

Input files

ReEVOLVER 1.0 requires 3 input files.

  1. a file containing the sequences of the putative gene and an outgroup sequence (example)
  2. a treefile in parenthesis format (example)
  3. a treefile in parenthesis format with a label for each branch [(1) time in MYA (2) number of observed stop codons (3) number of frameshifts indels] (example)

Running

ReEVOLVER 1.0 requires:

  1. the name of the input files
  2. the mutation and indel rates per site per million years
  3. the mutation rate per site per million years at CpG sites
  4. the number of simulations you wish to perform
  5. the softwares used to reconstruct the ancestral sequence at the time of the 1st speciation event
    (this reconstruction can be done using a maximum parsimony or a maximum likelihood approach (see Dupanloup and Kaessmann (submitted));
    the dnapars program of the PHYLIP package (Felsenstein 1996) and the codeml program of PAML (Yang 1997) are used respectively;
    these programs are provided in the archive files containing the ReEVOLVER software (see below)

ReEVOLVER 1.0 runs with the parsimony approach (for the reconstruction of ancestral sequences):

Click on the figure to get a pdf with a detailed description of the run !

ReEVOLVER 1.0 runs with the maximum likelihood approach (for the reconstruction of ancestral sequences):

Click on the figure to get a pdf file with a detailed description of the run !

Output files

ReEVOLVER 1.0 creates 4 output files.

  1. a logfile containing all information for each round of the simulations such as the inferred ancestral sequence, the number of observed substitutions along the different lineages of the species phylogeny, details about the simulations procedure
  2. the number of deleterious mutations (stop codons and indels) for each replicate
  3. the number of nonsynonymous and synonymous substitutions per replicate run,
  4. the test probabilities, Pdis and PNaNs (including associated information).

References

Download

  1. LINUX version (you will get a file (a tar archive compressed using gunzip) that contains all the files necessary for ReEVOLVER to run properly as well as examples; in this archive, the ReEVOLVER software is called Reevolver1.0_linux.out)
  2. Mac version (you will get a file (an archive compressed with winzip) that contains all the files necessary for ReEVOLVER to run properly as well as examples; in this archive, the ReEVOLVER software is called Reevolver1.0_mac.exe)
  3. WINDOWS version (you will get a file (an archive compressed with winzip) that contains all the files necessary for ReEVOLVER to run properly as well as examples; in this archive, the ReEVOLVER software is called Reevolver1.0_windows.exe)

Correspondence: Isabelle Dupanloup (1,2) and Henrik Kaessmann (1)
(1) Center for Integrative Genomics, University of Lausanne, Génopode, CH-1015 Lausanne, Switzerland
(2) Computational and Molecular Population Genetics Lab, Zoological Institute, University of Bern, 3012 Bern, Switzerland

E-mail: Isabelle.Dupanloup@zoo.unibe.ch and Henrik.Kaessmann@unil.ch