extended ouput to include theta_pi
removed unused-parameter flag
corrected calculation of Zengs E for folded spectra
parser API changed to constant parameters
parser API changed to constant parameters
parser API changed to constant parameters
parser API changed to constant parameters
alternative parser for ms output
alternative ms parser
This package contains implemented formulas for the calculation of the second and third moments of mutations described by a coalescent. Several utilities parse the output of the population-genetic simulation program "ms". The options listed here are not exhaustive. Further options are shown by calling the tools with option -h. nt2mom Prints the expected values of the second moments: E[xi_i xi_j]. Example: nt2mom 5 Comparison with simulations: ms 5 10000 -t 1 | msfs | fs2mom Optionally prints expection...
reformatted
added option for precision
modified help
changed variable names
transforms ms output to fastphase input
changed variable names
added ms2fastphase
added option to define precision
This package contains implemented formulas for the calculation of the second and third moments of mutations described by a coalescent. Several utilities parse the output of the population-genetic simulation program "ms". The options listed here are not exhaustive. Further options are shown by calling the tools with option -h. nt2mom Prints the expected values of the second moments: E[xi_i xi_j]. Example: nt2mom 5 Comparison with simulations: ms 5 10000 -t 1 | msfs | fs2mom Optionally prints expection...
subsets chromosomes in ms
minor code polishing
added mssub
This package contains implemented formulas for the calculation of the second and third moments of mutations described by a coalescent. Several utilities parse the output of the population-genetic simulation program "ms". The options listed here are not exhaustive. Further options are shown by calling the tools with option -h. nt2mom Prints the expected values of the second moments: E[xi_i xi_j]. Example: nt2mom 5 Comparison with simulations: ms 5 10000 -t 1 | msfs | fs2mom Optionally prints expection...
sorry for the late reply, the utilities here are intended only for piping, hence input is from STDIN and output to STDOUT
added ms2SF
ms to SweepFinder
added instructions
changed sample id format, added parameter check
corrected identation
updated references
This package contains implemented formulas for the calculation of the second and third moments of mutations described by a coalescent. Several utilities parse the output of the population-genetic simulation program "ms". The options listed here are not exhaustive. Further options are shown by calling the tools with option -h. nt2mom Prints the expected values of the second moments: E[xi_i xi_j]. Example: nt2mom 5 Comparison with simulations: ms 5 10000 -t 1 | msfs | fs2mom Optionally prints expection...
This package contains implemented formulas for the calculation of the second and third moments of mutations described by a coalescent. Several utilities parse the output of the population-genetic simulation program "ms". The options listed here are not exhaustive. Further options are shown by calling the tools with option -h. nt2mom Prints the expected values of the second moments: E[xi_i xi_j]. Example: nt2mom 5 Comparison with simulations: ms 5 10000 -t 1 | msfs | fs2mom Optionally prints expection...
remove duplicate positions
individuals start with number 1
This package contains implemented formulas for the calculation of the second and third moments of mutations described by a coalescent. Several utilities parse the output of the population-genetic simulation program "ms". The options listed here are not exhaustive. Further options are shown by calling the tools with option -h. nt2mom Prints the expected values of the second moments: E[xi_i xi_j]. Example: nt2mom 5 Comparison with simulations: ms 5 10000 -t 1 | msfs | fs2mom Optionally prints expection...
modified flag, added ms2vcf
translates ms output into vcf
corrected automatic smaple size recognition
extended to nested/disjoint spectra
added nested_nested etc.
renamed spectrum parts
renamed spectrum parts
changed signature
introduced smin smax
changed usage output
exit after usage text
added finer distinctions of mutations
added finer distinctions of mutations
moved calculation of y to tikz, added freq spec coloration
added journal
Merge branch 'master' of ssh://git.code.sf.net/p/coatli/code
This package contains implemented formulas for the calculation of the second and third moments of mutations described by a coalescent. Several utilities parse the output of the population-genetic simulation program "ms". The options listed here are not exhaustive. Further options are shown by calling the tools with option -h. nt2mom Prints the expected values of the second moments: E[xi_i xi_j]. Example: nt2mom 5 Comparison with simulations: ms 5 10000 -t 1 | msfs | fs2mom Optionally prints expection...
This package contains implemented formulas for the calculation of the second and third moments of mutations described by a coalescent. Several utilities parse the output of the population-genetic simulation program "ms". Further options are shown by calling the tools with option -h. nt2mom Prints the expected values of the second moments: E[xi_i xi_j]. Example: nt2mom 5 Comparison with simulations: ms 5 10000 -t 1 | msfs | fs2mom Optionally prints expection values conditional on a mutation of size...
This package contains implemented formulas for the calculation of the second and third moments of mutations described by a coalescent. Several utilities parse the output of the population-genetic simulation program "ms". nt2mom Prints the expected values of the second moments: E[xi_i xi_j]. Example: nt2mom 5 Comparison with simulations: ms 5 10000 -t 1 | msfs | fs2mom Optionally prints expection values conditional on a mutation of size k. Example: nt2mom 5 3 Comparison with simulations: ms 5 10000...
variabla naming conform to script
updated function names
minor changes
updated conform to c++-code
made skewness estimator unbiased
Merge branch 'master' of ssh://git.code.sf.net/p/coatli/code
undo part
replaced alpha expressions by alpha2
initialised all indices of alpha2 and beta2 to 0
changed order of expressions
renamed f and g to alpha2 and beta2
removed beta5
removed alpha2 and beta2
major rearrangement of terms
replaced partly beta6
readme
changed default output to inner-outer
changed sign of simple
removed bug in folded bal
added verbose output
removed bug
implemented 'simple' as omega
changed calculation of simple
added -simple
renamed inv to intro
This repository contains code for the calculation of 'neutrality test' using the...
This package contains implemented formulas for the calculation of the second and...
This package contains implemented formulas for the calculation of the second and...
This package contains implemented formulas for the calculation of the second and...
This package contains implemented formulas for the calculation of the second and...
This package contains implemented formulas for the calculation of the second and...
not needed
not needed
not needed
changed preamble
changed preamble
not needed
replaced by coatli
added verbose output
removed bug
minor refactoring
added verbose output
same as in coatli
allow for partial input spectrum
added folded spectrum
removed memory leak