coatli Activity
Second and third moments of the "Site frequency spectrum".
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Activity for coatli
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coatli released /coatli-1.0.6.tar.gz
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A. Klassmann committed [fce688]
parser API changed to constant parameters
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parser API changed to constant parameters
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parser API changed to constant parameters
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parser API changed to constant parameters
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alternative parser for ms output
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alternative ms parser
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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...
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reformatted
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added option for precision
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modified help
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transforms ms output to fastphase input
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changed variable names
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changed variable names
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added ms2fastphase
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added option to define precision
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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...
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subsets chromosomes in ms
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added mssub
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minor code polishing
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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...
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sorry for the late reply, the utilities here are intended only for piping, hence input is from STDIN and output to STDOUT
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added ms2SF
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ms to SweepFinder
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Wei Gao posted a comment on discussion General Discussion
I'm trying to use your package coatli to convert ms output into vcf. But when I use ms2vcf, I can't find how to set option of the input and output file. Could you please give me some comments about the command of ms2vcf? Thanks a lot.
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added instructions
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changed sample id format, added parameter check
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corrected identation
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updated references
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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...
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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...
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remove duplicate positions
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individuals start with number 1
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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...
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modified flag, added ms2vcf
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translates ms output into vcf
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extended to nested/disjoint spectra
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introduced smin smax
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changed usage output
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exit after usage text
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added finer distinctions of mutations
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added finer distinctions of mutations
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moved calculation of y to tikz, added freq spec coloration
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Merge branch 'master' of ssh://git.code.sf.net/p/coatli/code
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added journal
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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...
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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...
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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...
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variabla naming conform to script
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updated function names
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minor changes
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updated conform to c++-code
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made skewness estimator unbiased
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Merge branch 'master' of ssh://git.code.sf.net/p/coatli/code
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undo part
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replaced alpha expressions by alpha2
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initialised all indices of alpha2 and beta2 to 0
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changed order of expressions
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renamed f and g to alpha2 and beta2
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removed beta5
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removed alpha2 and beta2
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major rearrangement of terms
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replaced partly beta6
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This package contains implemented formulas for the calculation of the second and...
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This package contains implemented formulas for the calculation of the second and...
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This package contains implemented formulas for the calculation of the second and...
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This package contains implemented formulas for the calculation of the second and...
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This package contains implemented formulas for the calculation of the second and...
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removed memory leak
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removed init and delete of Harmonic numbers
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removed memory leak
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changed init of harmonic numbers
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changed summation order
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changed NESTED to NESTED_NESTED
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renamed variable
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added NESTED_NESTED
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changed NESTED into NESTED_NESTED
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changed command line arguments
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added -1 and -2 (output of linear/quadratic terms)
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added doc
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Mathematica package
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renamed function
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renamed variables
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changed signature of a2,b2
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corrected term in tbb
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added xaxis
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joined both lambda functions
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added multiple color function
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added option -2
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expanded tbbb
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renamed functions
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changed tbbb
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