scrm: Simulating the Evolution of Biological Sequences

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A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next-Generation Sequencing technologies for up to several thousand sequences.

Author
Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [aut, cph, ths], Gerton Lunter [aut, cph, ths]
Date of publication
2015-06-07 08:24:01
Maintainer
Paul Staab <develop@paulstaab.de>
License
GPL (>= 3)
Version
1.6.0-2
URLs

View on CRAN

Man pages

scrm
Simulate the evolution of biological sequences
scrm-package
Simulating the evolution of biological sequences

Files in this package

scrm
scrm/inst
scrm/inst/CITATION
scrm/inst/doc
scrm/inst/doc/scrm-TreesForApe.html
scrm/inst/doc/scrm-TreesForApe.Rmd
scrm/inst/doc/scrm-Arguments.html
scrm/inst/doc/scrm-Arguments.Rmd
scrm/inst/doc/scrm-TreesForApe.R
scrm/tests
scrm/tests/testthat.R
scrm/tests/testthat
scrm/tests/testthat/test-r_random-generator.R
scrm/tests/testthat/test-scrm.R
scrm/tests/testthat/test-summary-statistics.R
scrm/src
scrm/src/Makevars
scrm/src/summary_statistics.h
scrm/src/scrmr.cpp
scrm/src/scrm
scrm/src/scrm/event.h
scrm/src/scrm/random
scrm/src/scrm/random/fastfunc.h
scrm/src/scrm/random/random_generator.h
scrm/src/scrm/random/random_generator.cc
scrm/src/scrm/random/fastfunc.cc
scrm/src/scrm/tree_point.h
scrm/src/scrm/node.h
scrm/src/scrm/forest.h
scrm/src/scrm/param.cc
scrm/src/scrm/contemporaries_container.h
scrm/src/scrm/macros.h
scrm/src/scrm/model.h
scrm/src/scrm/model.cc
scrm/src/scrm/tree_point.cc
scrm/src/scrm/time_interval.cc
scrm/src/scrm/node_container.cc
scrm/src/scrm/node.cc
scrm/src/scrm/summary_statistics
scrm/src/scrm/summary_statistics/seg_sites.h
scrm/src/scrm/summary_statistics/seg_sites.cc
scrm/src/scrm/summary_statistics/oriented_forest.h
scrm/src/scrm/summary_statistics/tmrca.h
scrm/src/scrm/summary_statistics/tmrca.cc
scrm/src/scrm/summary_statistics/newick_tree.cc
scrm/src/scrm/summary_statistics/oriented_forest.cc
scrm/src/scrm/summary_statistics/summary_statistic.h
scrm/src/scrm/summary_statistics/frequency_spectrum.cc
scrm/src/scrm/summary_statistics/newick_tree.h
scrm/src/scrm/summary_statistics/frequency_spectrum.h
scrm/src/scrm/time_interval.h
scrm/src/scrm/forest.cc
scrm/src/scrm/node_container.h
scrm/src/scrm/param.h
scrm/src/r_random_generator.h
scrm/src/summary_statistics.cpp
scrm/src/test_exports.cpp
scrm/src/Makevars.win
scrm/src/RcppExports.cpp
scrm/NAMESPACE
scrm/NEWS
scrm/R
scrm/R/scrm.R
scrm/R/RcppExports.R
scrm/vignettes
scrm/vignettes/scrm-TreesForApe.Rmd
scrm/vignettes/scrm-Arguments.Rmd
scrm/README.md
scrm/MD5
scrm/build
scrm/build/vignette.rds
scrm/DESCRIPTION
scrm/man
scrm/man/scrm.Rd
scrm/man/scrm-package.Rd