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They include support for several models of nucleotide substitution as well as site-specific rate heterogeneity. Another program, SISSI (Gesell and Haeseler 2006), simulates site-specific interactions.None of these programs support insertions and deletions (indels). Although most programs typicallyuse biologically very simple indel simulation, some programsalso incorporate more advanced models for indel formation and distribution: SIMPROT (Pang et al.The output consists of the simulated genomes, multiple sequence alignments, and gene trees of all gene families, all ancestral sequences, the true species tree including LGTs, and for each pair of genomes the sets of orthologous, paralogous, and xenologous sequences.In future releases of ALF, we aim to incorporate more evolutionary models, including population-level events such as recombination. We first provide an overview of ALFs architecture and briefly describe how to set up a simulation scenario via ALFs web interface.In computational evolutionary biology, verification and benchmarking is a challenging task because the evolutionary history of studied biological entities is usually not known.Computer programs for simulating sequence evolution in silico have shown to be viable test beds for the verification of newly developed methods and to compare different algorithms.However, current simulation packages tend to focus either on gene-level aspects of genome evolution such as character substitutions and insertions and deletions (indels) or on genome-level aspects such as genome rearrangement and speciation events.
The ancestral genome may be represented by biological sequences supplied by the user or generated randomly according to user specifications.In this latter context, various simulation programs have been developed for different evolutionary models.Most of them simulate evolution at the gene or protein sequence level, as opposed to the genome level. 2000) offers functions for mutating sequences along a branch, including gaps.Thus, validation by simulation is often considered an insufficient but necessary step to propose a new method.Programs to simulate biological sequences can be divided into two main categories.