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data Added example_A1.R and data/mammals.nwk.
.gitignore
example_3_clean.R * Enabling plus*Gamma methods for all processes.
example_A1.R Minor comment fixes in example_A1.R
example_V2.1.1.R Added basic vignette examples.
example_V2.1.2.R Added basic vignette examples.
example_V2.2.R
example_V2.3.R Added basic vignette examples.
example_V2.4.1-2.R Added indel selection example: example_V2.4.3.R
example_V2.4.3.R Added indel selection example: example_V2.4.3.R
example_V2.5.R Added basic vignette examples.
example_V2.6.R
example_V2.7.R
example_V3.1.R
example_V3.2.R
example_V3.3.R Updated the names of the fasta files created by the vignette example …
example_V3.4.R
example_X1_plots.R
example_X2_tracks.R Added parallel replication vignette example.
example_X3_aln_length_tolerance.R Added parallel replication vignette example.
example_X4.R
example_X5.R
examples_class.R Moved some examples from the PhyloSim cosntrutor documentation
greg_scripts.R * Renamed example_plots.R to example_plots_X1_plots.R
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