Recent changes to Available Options

Available Options modified by Victor Spirin

Victor Spirin — Wed, 08 Jan 2014 17:04:49 -0000

--- v16
+++ v17
@@ -10,6 +10,7 @@
 --migMat (-m) <m\> migration rate from Population 2 to Population 1
 --selectionCoeff <s> selection coefficient for the selected locus
 --dominance <h\> sets heterozygous fitness to 1 + _hs_
+--dominanceBackground <h\> sets heterozygous fitness to 1 + _hs_ in neighboring regions
 --selectionStartSite <s1\> start of the region under selection
 --selectionEndSite <s2\> end of the region under selection
 --selectionRegionDensity (-SRD) <d\>  density of loci under selection in the region

Available Options modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 21:40:15 -0000

--- v15
+++ v16
@@ -17,8 +17,8 @@
 --fitnessTS fitness for truncation selection; fitness is 0 if number of mutations is greater than threshold
 --tThresh <t\> threshold parameter for truncation selection
 --fitnessSE fitness corresponding to synergistic epistasis
-\verb|--SEa | first parameter for synergistic epistasis\\
-\verb|--SEb | second parameter for synergistic epistasis\\
+--SEa <double\> first parameter for synergistic epistasis
+--SEb <double\> second parameter for synergistic epistasis
 --BURN (-B) <burn\> burnin time in units of 2N generations
 --tSpeciation (-TS) <tau\> run duration until speciation in units of 2N generations
 --tSweepStart (-TW) <tau\> run duration until start of sweep in units of 2N generations

Available Options modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 21:38:46 -0000

--- v14
+++ v15
@@ -15,16 +15,16 @@
 --selectionRegionDensity (-SRD) <d\>  density of loci under selection in the region
 --fitnessBoolOR  fitness is 1 + _s_ if we have any of the alleles in the selected region
 --fitnessTS fitness for truncation selection; fitness is 0 if number of mutations is greater than threshold
-\verb|--tThresh | threshold parameter for truncation selection\\
+--tThresh <t\> threshold parameter for truncation selection
 --fitnessSE fitness corresponding to synergistic epistasis
 \verb|--SEa | first parameter for synergistic epistasis\\
 \verb|--SEb | second parameter for synergistic epistasis\\
---BURN (-B) <burn\> burnin time in units of 2 _N_ generations
-\verb|--tSpeciation (-TS) | run duration until speciation in units of $2N$ generations\\
---tSweepStart (-TW) <tau\> run duration until start of sweep in units of 2 _N_ generations
+--BURN (-B) <burn\> burnin time in units of 2N generations
+--tSpeciation (-TS) <tau\> run duration until speciation in units of 2N generations
+--tSweepStart (-TW) <tau\> run duration until start of sweep in units of 2N generations
 -Tg P <p\> <tau\> <alpha\> P <p\> <tau\> <alpha\>  population growth start time and rate
---tTotal (-TE) <tau\> total run duration after burnin in units of 2 _N_ generations
+--tTotal (-TE) <tau\> total run duration after burnin in units of 2N generations
 --sampSize (-n) <SS1\> \[<SS2\>\] sample size for output
---outputTime <tau1\> \[<tau2\>...<taun\>\]  output times after burnin in units of 2 _N_ generations
+--outputTime <tau1\> \[<tau2\>...<taun\>\]  output times after burnin in units of 2N generations
 --outfile (-o) <file\> output file prefix

Available Options modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 21:36:38 -0000

--- v13
+++ v14
@@ -10,8 +10,8 @@
 --migMat (-m) <m\> migration rate from Population 2 to Population 1
 --selectionCoeff <s> selection coefficient for the selected locus
 --dominance <h\> sets heterozygous fitness to 1 + _hs_
-\verb|--selectionStartSite | start of the region under selection\\
-\verb|--selectionEndSite | end of the region under selection\\
+--selectionStartSite <s1\> start of the region under selection
+--selectionEndSite <s2\> end of the region under selection
 --selectionRegionDensity (-SRD) <d\>  density of loci under selection in the region
 --fitnessBoolOR  fitness is 1 + _s_ if we have any of the alleles in the selected region
 --fitnessTS fitness for truncation selection; fitness is 0 if number of mutations is greater than threshold

Available Options modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 21:24:26 -0000

--- v12
+++ v13
@@ -12,14 +12,14 @@
 --dominance <h\> sets heterozygous fitness to 1 + _hs_
 \verb|--selectionStartSite | start of the region under selection\\
 \verb|--selectionEndSite | end of the region under selection\\
-\verb|--selectionRegionDensity (-SRD) | density of loci under selection in the region\\
+--selectionRegionDensity (-SRD) <d\>  density of loci under selection in the region
 --fitnessBoolOR  fitness is 1 + _s_ if we have any of the alleles in the selected region
---fitnessTS fitness for truncation selection, fitness is 0 if number of mutation greater than threshold
+--fitnessTS fitness for truncation selection; fitness is 0 if number of mutations is greater than threshold
 \verb|--tThresh | threshold parameter for truncation selection\\
 --fitnessSE fitness corresponding to synergistic epistasis
 \verb|--SEa | first parameter for synergistic epistasis\\
 \verb|--SEb | second parameter for synergistic epistasis\\
-\verb|--BURN (-B) | burnin time in units of $2N$ generations\\
+--BURN (-B) <burn\> burnin time in units of 2 _N_ generations
 \verb|--tSpeciation (-TS) | run duration until speciation in units of $2N$ generations\\
 --tSweepStart (-TW) <tau\> run duration until start of sweep in units of 2 _N_ generations
 -Tg P <p\> <tau\> <alpha\> P <p\> <tau\> <alpha\>  population growth start time and rate

Available Options modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 21:21:52 -0000

--- v11
+++ v12
@@ -13,18 +13,18 @@
 \verb|--selectionStartSite | start of the region under selection\\
 \verb|--selectionEndSite | end of the region under selection\\
 \verb|--selectionRegionDensity (-SRD) | density of loci under selection in the region\\
-\verb|--fitnessBoolOR| fitness is $1+s$ if we have any of the alleles in the selected region\\
+--fitnessBoolOR  fitness is 1 + _s_ if we have any of the alleles in the selected region
 --fitnessTS fitness for truncation selection, fitness is 0 if number of mutation greater than threshold
 \verb|--tThresh | threshold parameter for truncation selection\\
---fitnessSE fitness corresponding to synergistic epistasis
+--fitnessSE fitness corresponding to synergistic epistasis
 \verb|--SEa | first parameter for synergistic epistasis\\
 \verb|--SEb | second parameter for synergistic epistasis\\
 \verb|--BURN (-B) | burnin time in units of $2N$ generations\\
 \verb|--tSpeciation (-TS) | run duration until speciation in units of $2N$ generations\\
---tSweepStart (-TW) <tau\> run duration until start of sweep in units of 2_N_ generations
+--tSweepStart (-TW) <tau\> run duration until start of sweep in units of 2 _N_ generations
 -Tg P <p\> <tau\> <alpha\> P <p\> <tau\> <alpha\>  population growth start time and rate
---tTotal (-TE) <tau\> total run duration after burnin in units of 2_N_ generations
+--tTotal (-TE) <tau\> total run duration after burnin in units of 2 _N_ generations
 --sampSize (-n) <SS1\> \[<SS2\>\] sample size for output
---outputTime <tau1\> \[<tau2\>...<taun\>\]  output times after burnin in units of 2_N_ generations
+--outputTime <tau1\> \[<tau2\>...<taun\>\]  output times after burnin in units of 2 _N_ generations
 --outfile (-o) <file\> output file prefix

Available Options modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 21:18:26 -0000

--- v10
+++ v11
@@ -9,22 +9,22 @@
 --rho (-r) \[P <p\>\]  recombination rate per site
 --migMat (-m) <m\> migration rate from Population 2 to Population 1
 --selectionCoeff <s> selection coefficient for the selected locus
-\verb|--dominance | sets heterozygous fitness to 1+hs\\
+--dominance <h\> sets heterozygous fitness to 1 + _hs_
 \verb|--selectionStartSite | start of the region under selection\\
 \verb|--selectionEndSite | end of the region under selection\\
 \verb|--selectionRegionDensity (-SRD) | density of loci under selection in the region\\
 \verb|--fitnessBoolOR| fitness is $1+s$ if we have any of the alleles in the selected region\\
-\verb|--fitnessTS| fitness for truncation selection, fitness is 0 if number of mutation greater than threshold\\
+--fitnessTS fitness for truncation selection, fitness is 0 if number of mutation greater than threshold
 \verb|--tThresh | threshold parameter for truncation selection\\
-\verb|--fitnessSE| fitness corresponding to synergistic epistasis\\
+--fitnessSE fitness corresponding to synergistic epistasis
 \verb|--SEa | first parameter for synergistic epistasis\\
 \verb|--SEb | second parameter for synergistic epistasis\\
 \verb|--BURN (-B) | burnin time in units of $2N$ generations\\
 \verb|--tSpeciation (-TS) | run duration until speciation in units of $2N$ generations\\
-\verb|--tSweepStart (-TW) | run duration until start of sweep in units of $2N$ generations\\
+--tSweepStart (-TW) <tau\> run duration until start of sweep in units of 2_N_ generations
 -Tg P <p\> <tau\> <alpha\> P <p\> <tau\> <alpha\>  population growth start time and rate
---tTotal (-TE) <tau\> total run duration after burnin in units of 2N generations
+--tTotal (-TE) <tau\> total run duration after burnin in units of 2_N_ generations
 --sampSize (-n) <SS1\> \[<SS2\>\] sample size for output
---outputTime <tau1\> \[<tau2\>...<taun\>\]  output times after burnin in units of 2N generations
+--outputTime <tau1\> \[<tau2\>...<taun\>\]  output times after burnin in units of 2_N_ generations
 --outfile (-o) <file\> output file prefix

Available Options modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 21:09:32 -0000

--- v9
+++ v10
@@ -6,8 +6,8 @@
 --length (-L) <genome_length\>  genome length, base pairs
 --popSize (-N) \[P <p>\]  population size
 --theta (-t) \[P <p\>\]   mutation rate per site
-\verb|--rho (-r) \[P \\] | recombination rate per site\\
-\verb|--migMat (-m) | migration rate from Population 2 to Population 1\\
+--rho (-r) \[P <p\>\]  recombination rate per site
+--migMat (-m) <m\> migration rate from Population 2 to Population 1
 --selectionCoeff <s> selection coefficient for the selected locus
 \verb|--dominance | sets heterozygous fitness to 1+hs\\
 \verb|--selectionStartSite | start of the region under selection\\
@@ -23,8 +23,8 @@
 \verb|--tSpeciation (-TS) | run duration until speciation in units of $2N$ generations\\
 \verb|--tSweepStart (-TW) | run duration until start of sweep in units of $2N$ generations\\
 -Tg P <p\> <tau\> <alpha\> P <p\> <tau\> <alpha\>  population growth start time and rate
-\verb|--tTotal (-TE) | total run duration after burnin in units of $2N$ generations\\
+--tTotal (-TE) <tau\> total run duration after burnin in units of 2N generations
 --sampSize (-n) <SS1\> \[<SS2\>\] sample size for output
 --outputTime <tau1\> \[<tau2\>...<taun\>\]  output times after burnin in units of 2N generations
-\verb|--outfile (-o) | output file prefix
+--outfile (-o) <file\> output file prefix

Available Options modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 21:06:15 -0000

--- v8
+++ v9
@@ -1,9 +1,9 @@
 List of available options
 ==========

-\verb|--help (-h)| print help message\\
-\verb|--seed (-s) | random seed\\
-\verb|--length (-L) | genome length, base pairs\\
+--help (-h) print help message
+--seed (-s) <int\>  random seed
+--length (-L) <genome_length\>  genome length, base pairs
 --popSize (-N) \[P <p>\]  population size
 --theta (-t) \[P <p\>\]   mutation rate per site
 \verb|--rho (-r) \[P \\] | recombination rate per site\\
@@ -24,7 +24,7 @@
 \verb|--tSweepStart (-TW) | run duration until start of sweep in units of $2N$ generations\\
 -Tg P <p\> <tau\> <alpha\> P <p\> <tau\> <alpha\>  population growth start time and rate
 \verb|--tTotal (-TE) | total run duration after burnin in units of $2N$ generations\\
-\verb|--sampSize (-n)  []| sample size for output\\
+--sampSize (-n) <SS1\> \[<SS2\>\] sample size for output
 --outputTime <tau1\> \[<tau2\>...<taun\>\]  output times after burnin in units of 2N generations
 \verb|--outfile (-o) | output file prefix

Available Options modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 21:03:11 -0000

--- v7
+++ v8
@@ -25,6 +25,6 @@
 -Tg P <p\> <tau\> <alpha\> P <p\> <tau\> <alpha\>  population growth start time and rate
 \verb|--tTotal (-TE) | total run duration after burnin in units of $2N$ generations\\
 \verb|--sampSize (-n)  []| sample size for output\\
-\verb|--outputTime  [...]| output times after burnin in units of $2N$ generations\\
+--outputTime <tau1\> \[<tau2\>...<taun\>\]  output times after burnin in units of 2N generations
 \verb|--outfile (-o) | output file prefix