Provided by: indelible_1.03-4build1_amd64 bug


       indelible - powerful and flexible simulator of biological evolution



       No options can be passed via the commandline.


       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


       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.

              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

       [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

              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.

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


       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


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