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data Added example_A1.R and data/mammals.nwk. Jan 24, 2011
.gitignore Some .gitignore updates. Sep 21, 2010
example_3_clean.R * Enabling plus*Gamma methods for all processes. Sep 27, 2010
example_A1.R Minor comment fixes in example_A1.R Jan 27, 2011
example_V2.1.1.R Added basic vignette examples. Oct 26, 2010
example_V2.1.2.R
example_V2.2.R Added basic vignette examples. Oct 26, 2010
example_V2.3.R Added basic vignette examples. Oct 26, 2010
example_V2.4.1-2.R
example_V2.4.3.R Added indel selection example: example_V2.4.3.R Nov 2, 2010
example_V2.5.R Added basic vignette examples. Oct 26, 2010
example_V2.6.R Vignette fix: replication -> replicate. Jun 28, 2011
example_V2.7.R Vignette fix: replication -> replicate. Jun 28, 2011
example_V3.1.R Updated the names of the fasta files created by the vignette example … Jan 19, 2011
example_V3.2.R
example_V3.3.R
example_V3.4.R Updated the names of the fasta files created by the vignette example … Jan 19, 2011
example_X1_plots.R Added #! to example_X1_plots.R Jan 24, 2011
example_X2_tracks.R Added parallel replication vignette example. Jun 28, 2011
example_X3_aln_length_tolerance.R Added parallel replication vignette example. Jun 28, 2011
example_X4.R
example_X5.R Added example for ToleranceSubstitution. Apr 25, 2014
examples_class.R Moved some examples from the PhyloSim cosntrutor documentation Sep 7, 2012
greg_scripts.R
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