PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

BMC Bioinformatics

Table 1 Comparison of some advanced alignment simulation tools

Key	Feature*	Dawg v1.1.2	MySSP v1.0	Indel-Seq-Gen v1.0.3	SIMPROT v1.01	INDELible v1.0	PhyloSim v0.12
II	GTR	•	•			•	•
II	UNREST					•	•
II	Empirical amino acid models			3	3	15	11
II	User defined amino acid models					•	•
II	Codon models					•	•
III	Combinations of substitution processes						•
IV	Discrete gamma					•	•
IV	Continuous gamma	•	•		•	•	•
IV	Proportion of invariant sites	•		•		•	•
V	Complex rate variation						•
VI	Multiple indel processes						•
VII	Rate variation with indel processes						•
VIII	Selective constraints on indels						•
IX	Partitions		•	•	•	•	•
X	Non-homogeneous evolution		•			•	•
XI	Full control over inserts						•

Availability of complex evolutionary processes in different simulation software. Additional details for less advanced software and simpler models are given by [[12], Table 1].
*See text for details.

ISSN: 1471-2105