Recent changes to Compilation and Running

Compilation and Running modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 22:55:25 -0000

--- v8
+++ v9
@@ -1,7 +1,7 @@
 Compilation and running 
 =========================

-=== Compiling the code ===
+Compiling the code

 The code can be compiled simply with the command g++ -O3 \*.cc.  This will create a.out executable.  A Makefile is included; simply typing make creates executable FS.

@@ -9,7 +9,7 @@

 The output will contain log file with the parameters of the simulation, vcf file for Population 1, and the allele frequency distribution file for Population 1.

-=== Output ===
+Output

 The output file names are specified by command line argument -o followed by file name root.  For example, ./FS -o fs1 will create the following files in the working directory:

Compilation and Running modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 22:53:54 -0000

--- v7
+++ v8
@@ -14,8 +14,8 @@
 The output file names are specified by command line argument -o followed by file name root.  For example, ./FS -o fs1 will create the following files in the working directory:

 fs1.log
-\verb|fs1.sequences.population1.burnin.vcf|\\
-\verb|fs1.derivedAlleleFrequency.population1.burnin|\\
+fs1.sequences.population1.burnin.vcf
+fs1.derivedAlleleFrequency.population1.burnin
 ...
-\verb|fs1.sequences.population1.final.vcf|\\
-\verb|fs1.derivedAlleleFrequency.population1.final|\\
+fs1.sequences.population1.final.vcf
+fs1.derivedAlleleFrequency.population1.final

Compilation and Running modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 22:52:00 -0000

--- v6
+++ v7
@@ -1,4 +1,5 @@
-= Compilation and running =
+Compilation and running 
+=========================

 === Compiling the code ===

@@ -10,11 +11,11 @@

 === Output ===

-The output file names are specified by command line argument \verb|-o| followed by file name root.  For example, \verb|./FS -o fs1| will create the following files in the working directory:
+The output file names are specified by command line argument -o followed by file name root.  For example, ./FS -o fs1 will create the following files in the working directory:

-\verb|fs1.log|\\
+fs1.log
 \verb|fs1.sequences.population1.burnin.vcf|\\
 \verb|fs1.derivedAlleleFrequency.population1.burnin|\\
-$$\cdots$$
+...
 \verb|fs1.sequences.population1.final.vcf|\\
 \verb|fs1.derivedAlleleFrequency.population1.final|\\

Compilation and Running modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 22:48:51 -0000

--- v5
+++ v6
@@ -1,5 +1,4 @@
-Compilation and running
-========================
+= Compilation and running =

 === Compiling the code ===

Compilation and Running modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 22:47:17 -0000

--- v4
+++ v5
@@ -1,7 +1,7 @@
 Compilation and running
 ========================

-===Compiling the code===
+=== Compiling the code ===

 The code can be compiled simply with the command g++ -O3 \*.cc.  This will create a.out executable.  A Makefile is included; simply typing make creates executable FS.

@@ -9,11 +9,10 @@

 The output will contain log file with the parameters of the simulation, vcf file for Population 1, and the allele frequency distribution file for Population 1.

-===Output===
+=== Output ===

-The output file names are specified by command line argument
-\verb|-o| followed by file name root.  For example, \verb|./FS -o fs1|
-will create the following files in the working directory:\\
+The output file names are specified by command line argument \verb|-o| followed by file name root.  For example, \verb|./FS -o fs1| will create the following files in the working directory:
+
 \verb|fs1.log|\\
 \verb|fs1.sequences.population1.burnin.vcf|\\
 \verb|fs1.derivedAlleleFrequency.population1.burnin|\\

Compilation and Running modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 22:44:47 -0000

--- v3
+++ v4
@@ -1,8 +1,22 @@
 Compilation and running
 ========================

+===Compiling the code===
+
 The code can be compiled simply with the command g++ -O3 \*.cc.  This will create a.out executable.  A Makefile is included; simply typing make creates executable FS.

-To run with default parameters, simply type ./FS in the current working directory.  The default parameters correspond to one population of 10,000 individuals evolving for 4 x 2N = 80,000 generations with mutation rate $\mu=10^{-8}$, recombination rate _r_ = 10^-8, under no selection (random drift).  This is a default burnin period.  The run time is about 30 minutes on an 1.8GHz processor.  
+To run with default parameters, simply type ./FS in the current working directory.  The default parameters correspond to one population of 10,000 individuals evolving for 4 x 2N = 80,000 generations with mutation rate µ = 10^-8, recombination rate _r_ = 10^-8, under no selection (random drift).  This is a default burnin period.  The run time is about 30 minutes on an 1.8GHz processor.  

 The output will contain log file with the parameters of the simulation, vcf file for Population 1, and the allele frequency distribution file for Population 1.
+
+===Output===
+
+The output file names are specified by command line argument
+\verb|-o| followed by file name root.  For example, \verb|./FS -o fs1|
+will create the following files in the working directory:\\
+\verb|fs1.log|\\
+\verb|fs1.sequences.population1.burnin.vcf|\\
+\verb|fs1.derivedAlleleFrequency.population1.burnin|\\
+$$\cdots$$
+\verb|fs1.sequences.population1.final.vcf|\\
+\verb|fs1.derivedAlleleFrequency.population1.final|\\

Compilation and Running modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 22:32:57 -0000

--- v2
+++ v3
@@ -1,10 +1,8 @@
 Compilation and running
 ========================

-The code can be compiled simply with the command g++ -O3 \*.cc.  This will create a.out executable.  A Makefile is included; simply typing make creates
-executable FS.
+The code can be compiled simply with the command g++ -O3 \*.cc.  This will create a.out executable.  A Makefile is included; simply typing make creates executable FS.

-To run with default parameters, simply type ./FS in the current working directory.  The default parameters correspond to one population of 10,000 individuals evolving for $4\times 2N=80,000$
-generations with mutation rate $\mu=10^{-8}$, recombination rate $r=10^{-8}$, under no selection (random drift).  This is a default burnin period.  The run time is about 30 minutes on an 1.8GHz processor.  
+To run with default parameters, simply type ./FS in the current working directory.  The default parameters correspond to one population of 10,000 individuals evolving for 4 x 2N = 80,000 generations with mutation rate $\mu=10^{-8}$, recombination rate _r_ = 10^-8, under no selection (random drift).  This is a default burnin period.  The run time is about 30 minutes on an 1.8GHz processor.  

-The output will contain log file with the parameters of the simulation, vcf file for Population 1, and the allele frequency distribution file for Population 1.
+The output will contain log file with the parameters of the simulation, vcf file for Population 1, and the allele frequency distribution file for Population 1.

Compilation and Running modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 22:30:40 -0000

--- v1
+++ v2
@@ -1,19 +1,10 @@
 Compilation and running
 ========================

-The code can be compiled simply with the command
-g++ -O3 \*.cc  This will create a.out executable.  A
-Makefile is included; simply typing make creates
+The code can be compiled simply with the command g++ -O3 \*.cc.  This will create a.out executable.  A Makefile is included; simply typing make creates
 executable FS.

-To run with default parameters, simply type \verb|./FS| in the current
-working directory.  The default parameters correspond to one
-population of 10,000 individuals evolving for $4\times 2N=80,000$
-generations with mutation rate $\mu=10^{-8}$, recombination rate
-$r=10^{-8}$, under no selection (random drift).  This is a default
-burnin period.  The run time is about 30 minutes on an 1.8GHz
-processor.  
+To run with default parameters, simply type ./FS in the current working directory.  The default parameters correspond to one population of 10,000 individuals evolving for $4\times 2N=80,000$
+generations with mutation rate $\mu=10^{-8}$, recombination rate $r=10^{-8}$, under no selection (random drift).  This is a default burnin period.  The run time is about 30 minutes on an 1.8GHz processor.  

-The output will contain log file with the parameters of the
-simulation, vcf file for Population 1, and the allele frequency
-distribution file for Population 1.
+The output will contain log file with the parameters of the simulation, vcf file for Population 1, and the allele frequency distribution file for Population 1.

Compilation and Running modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 22:27:46 -0000

Compilation and running

The code can be compiled simply with the command
g++ -O3 *.cc This will create a.out executable. A
Makefile is included; simply typing make creates
executable FS.

To run with default parameters, simply type \verb|./FS| in the current
working directory. The default parameters correspond to one
population of 10,000 individuals evolving for $4\times 2N=80,000$
generations with mutation rate $\mu=10^{-8}$, recombination rate
$r=10^{-8}$, under no selection (random drift). This is a default
burnin period. The run time is about 30 minutes on an 1.8GHz
processor.

The output will contain log file with the parameters of the
simulation, vcf file for Population 1, and the allele frequency
distribution file for Population 1.