xenial (1) indelible.1.gz

Provided by: indelible_1.03-2_amd64 bug

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 continous 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 © 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.