Simulating Sequence Evolution with Site-Specific Interactions. SISSI is a software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices.

The program SISSI (Simulating Site-Specific Interactions along Phylogentic Trees) is a software tool which generates any number of data sets of related sequences with site-specific interactions for a given phylogeny, user defined sytems of neighbourhoods and instantaneous rate matrices.

SISSI incorporating site-specific interactions complements the available simulation approach. The basic idea is to use separate models for each site defined by the interactions with other sites in the sequence.

It follows that the rates of substitution may be not only variable in time (rate heterogeneity), but also correlated. With different null models, specific annotations and adequate parameters for the neighbourhoods, there are a lot of models imaginable for this simulation procedure, which will by and by implemented in SISSI.

SISSI is a command-line program which allows users to specify the parameter values.

The license of this software is Freeware, you can free download and free use this calculator software.