NAME

       indelible - powerful and flexible simulator of biological evolution

SYNOPSIS

       indelible

       No options can be passed via the commandline.

DESCRIPTION

       indelible  can  simulate  evolution  of multi-partitioned nucleotide, amino-acid, or codon
       data sets through the processes of insertion, deletion,  and  substitution  in  continuous
       time. All common evolutionary models are supported.

       The      full      documentation      for      indelible      is      available      under
       /usr/share/doc/indelible/help/index.html.

CONFIGURATION

       indelible reads the settings for a simulation run from a file  named  control.txt  in  the
       current  directory.  The  file  is  split  into  blocks,  with  each block controlling one
       particular aspect of the simulation. Blocks may contain further sub-blocks.  Comments  can
       be  given  in  C or C++ style. If indelible is executed without a control file present, an
       example file is generated.

       [TYPE] type
              Every control file must begin with a TYPE block. The possible types are NUCLEOTIDE,
              AMINOACID, and CODON.

       [SETTINGS]
              This  block  specifies non-essential user preferences such as output file types and
              formats, seeds for the random number generator,  and  whether  to  output  detailed
              reports.

       [MODEL] modelname
              This  block  starts  a  new  evolutionary  model  to  be  used  for simulation. The
              particular parameters including substitution  models,  indel-rates  and  codon-site
              models are controlled via submodels. modelname can be any name of your choosing.

       [TREE] treename newick
              This  block  is  used  to  specify  a  guide-tree  with  the  given  name treename.
              Evolutionary distances are represented as branch lengths for  the  tree  in  NEWICK
              format.

       [BRANCHES]
              These  blocks  are  used  to  simulate non-stationary and non-homogenous processes.
              Different models can be specified on different branches of the guide-tree  allowing
              branches  to have different models of substitution, indel length distribution, rate
              heterogeneity, base composition etc.

       [PARTITIONS] partitionname
              During each run multiple sequence partitions can be simulated. For  each  partition
              the guide-tree, evolutionary model and sequence length has to be specified.

       [EVOLVE]
              Within this block multiple replicas of a partition may be generated.

COPYRIGHT

       Copyright © 2010 William Fletcher License GPLv3+: GNU GPL version 3 or later.
       This  is free software: you are free to change and redistribute it.  There is NO WARRANTY,
       to  the  extent  permitted  by   law.    The   full   license   text   is   available   at
       <http://gnu.org/licenses/gpl.html>.

ACKNOWLEDGMENTS

       William  Fletcher  and  Ziheng  Yang (2009). INDELible: A Flexible Simulator of Biological
       Sequence Evolution, Molecular Biology and Evolution, 26(8):1879-1888.