Testing for covarion evolution
Testing for covarion-like evolution in protein sequences Wang, H.-C., Spencer, M., Susko, E. and Roger, A.J. (2007). Molecular Biology and Evolution 24: 294-305 (the authoritative version is here).
seq-gen-aminocov Tar archive of C code for simulating the Tuffley and Steel (1998)/Huelsenbeck (2002) and Galtier (2001) covarion models of nucleotide and amino acid evolution.
Version 1.3, 17/11/11. Lars Jermiin fixed an error in setState (evolve.c) that could result in array overflow, added the MtArt model, and made minor cosmetic changes.
Version 1.2, 15/05/08. Bug fix: hidden states were printed wrongly using the -wh option when there were multiple partitions (the states were still used correctly in the simulation). Thanks to Liat Shavit-Grievink for reporting this. Also fixed some inherited memory leaks and compiler warnings.
New in version 1.1: a general model of which the Huelsenbeck and Galtier models are special cases. Based on seq-gen-cov by Cécile Ané (the Tuffley and Steel/Huelsenbeck model for nucleotides: Ané et al 2005) and seq-gen by Andrew Rambaut and Nick Grassly (non-covarion models for nucleotides and amino acids: Rambaut and Grassly 1997). See readme.txt for details.
stochmap1.0.tar.gz Software for using stochastic mapping to detect deviations of data from covarion (and other evolutionary) models.
Ané, C., Burleigh, J.G., McMahon, M.M. and Sanderson, M.J. (2005). Covarion structure in plastid genome evolution: a new statistical test. Molecular Biology and Evolution 22(4): 914-924.
Galtier, N. (2001). Maximum-likelihood phylogenetic analysis under a covarion-like model. Molecular Biology and Evolution 18(5): 866-873.
Huelsenbeck, J.P. (2002). Testing a covariotide model of DNA substitution. Molecular Biology and Evolution 19(5): 698-707.
Rambaut, A. and Grassly, N.C. (1997). Seq-Gen: an application for the Monte-Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in Bioscience 13: 235-238.
Tuffley, C. and Steel, M. (1998). Modeling the covarion hypothesis of nucleotide substitution. Mathematical Biosciences 147: 63-91.