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arlequin [2007/12/03 16:40] – heidiarlequin [2011/07/07 11:16] (current) – heidi
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 \\ \\
-**[[http://cmpg.unibe.ch/software/arlequin3/|Arlequin]]**+**[[http://popgen.unibe.ch/software/arlequin35/|Arlequin]]**\\ 
 +[[http://popgen.unibe.ch/software/arlequin35/man/Arlequin35.pdf|manual]] 
  
 \\ \\
-Arlequin ver 3.11 (released 19 February 2007)\\+Arlequin ver 3.5 (released 24 February 2010)\\
 The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples.\\ The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples.\\
-The analyses Arlequin can perform on the data fall into two main categories: intra-population and inter-population methods.+The analyses Arlequin can perform on the data fall into two main categories: intra-population and inter-population methods.\\ 
 +Computes indices of genetic diversity, F-statistics and genetic distances between populations; exact test of HWE, LD and population differentiation; tests selective neutrality within populations; Mantel test; estimates gametic phase from multilocus genotypes; estimated demographic parameters form mismatch distribution 
 + 
 + 
 ===== Program information ===== ===== Program information =====
   * program written in C++   * program written in C++
-  * Windows version (2000, XP, and above)+  * Windows version (XP, Vista, 7) 
 +  * LINUX
  
 \\ \\
 +
 ===== Data type handled ===== ===== Data type handled =====
   * DNA sequences   * DNA sequences
   * RFLP   * RFLP
 +  * SNP
   * Microsattelite   * Microsattelite
   * Standard data   * Standard data
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 \\ \\
 +
 +
  
  
 ===== Input Files ===== ===== Input Files =====
-Contain the description of the properties of the data, as well as the raw data themselves.+Contain the description of the properties of the data, as well as the raw data themselves. The input files should have a "*.arp" extension (for ARlequin Project).
  
 \\ \\
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 \\ \\
 +
 +==== example: ====
 The following small example is a project file containing four populations. The data type is STANDARD genotypic data with unknown gametic phase:  The following small example is a project file containing four populations. The data type is STANDARD genotypic data with unknown gametic phase: 
 <code> <code>
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   }    } 
 </code> </code>
 +
  
  
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 ==== Profile section: ==== ==== Profile section: ====
-  * Title (string within “”): <code>Title=”title xy”</code> +  * Title (string within “”): ''Title=”title xy”'' 
-  * Number of samples (int 1-1000):  <code>NbSamples =3</code> +  * Number of samples (int 1-1000): ''NbSamples =3'' 
-  * Type of data (DNA, RFLP, MICROSAT, STANDARD, FREQUENCY): <code>DataType = DNA</code> +  * Type of data (DNA, RFLP, MICROSAT, STANDARD, FREQUENCY): ''DataType = DNA'' 
-  * Haplotypic/genotypic data (0/1): <code>GenotypicData = 0</code>+  * Haplotypic/genotypic data (0/1): ''GenotypicData = 0''
 \\  \\ 
   * Optionally (__default value__):   * Optionally (__default value__):
-    * locus separator (__WHITESPACE__, TAB, NONE, …): <code>LocusSeparator = TAB</code> +    * locus separator (__WHITESPACE__, TAB, NONE, …): ''LocusSeparator = TAB'' 
-    * gametic phase known/unknown (__1__/0): <code>GameticPhase = 1</code> +    * gametic phase known/unknown (__1__/0): ''GameticPhase = 1'' 
-    * recessive/ co-dominant allele (1/__0__): <code>RecessiveData = 1</code> +    * recessive/ co-dominant allele (1/__0__): ''RecessiveData = 1'' 
-    * code for recessive allele (string within __“null”__): <code>RecessiveAllel =”xxx”</code> +    * code for recessive allele (string within __“null”__): ''RecessiveAllel =”xxx”'' 
-    * code for missing data (character within __“?”__ or __‘?’__): <code>MissingData = ‘$’</code> +    * code for missing data (character within __“?”__ or __‘?’__): ''MissingData = ‘$’'' 
-    * frequencies as absolute/relative values (__ABS__/REL): <code>Frequency = ABS</code> +    * frequencies as absolute/relative values (__ABS__/REL): ''Frequency = ABS'' 
-    * significant digits for haplotype frequency outputs (real number 1e-2 – 1e-7(__1e-5__)): <code>FrequencyThreshold = 0.00001</code>  +    * significant digits for haplotype frequency outputs (real number 1e-2 – 1e-7(__1e-5__)): ''FrequencyThreshold = 0.00001''  
-    * convergence criterion for the EM algorithm (real number __1e-7__ – 1e-12): <code>EpsilonValue = 1e-10</code>+    * convergence criterion for the EM algorithm (real number __1e-7__ – 1e-12): ''EpsilonValue = 1e-10'' 
 + 
 + 
 + 
  
  
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 === Samples (obligatory): === === Samples (obligatory): ===
 Defines haplotypic/genotypic content of the different samples Defines haplotypic/genotypic content of the different samples
-  * name for each sample (string within “”): <code>SampleName = “name xy”</code> +  * name for each sample (string within “”): ''SampleName = “name xy”'' 
-  * size of sample (int value): <code>SampleSize = 732</code>+  * size of sample (int value): ''SampleSize = 732''
   * data itself (list of haplotypes or genotypes and their frequencies, entered with braces):    * data itself (list of haplotypes or genotypes and their frequencies, entered with braces): 
 <code> <code>
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 specifies the hierarchical genetic structure of the samples. It is possible to define groups of populations. specifies the hierarchical genetic structure of the samples. It is possible to define groups of populations.
   * start of the subsection: <code>[[Structure]]</code>   * start of the subsection: <code>[[Structure]]</code>
-  * name for the genetic structure (string within ""): <code>StructureName = "A example"</code> +  * name for the genetic structure (string within ""): ''StructureName = "A example"'' 
-  * number of groups defined in the structure (int value): <code>NbGroups = 5</code>+  * number of groups defined in the structure (int value): ''NbGroups = 5''
   * group definitions (list containing the names of the samples belonging to the group, entered within braces):   * group definitions (list containing the names of the samples belonging to the group, entered within braces):
 <code> <code>
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 allows to specify some distance matrices. The goal is to compute a correlation between the Ymatrix and X1 or a partial correlation between the Ymatrix, X1 and X2. The Ymatrix can be either a pairwise population FST matrix or a custom matrix entered into the project by the user. X1 (and X2) have to be defined in the project. allows to specify some distance matrices. The goal is to compute a correlation between the Ymatrix and X1 or a partial correlation between the Ymatrix, X1 and X2. The Ymatrix can be either a pairwise population FST matrix or a custom matrix entered into the project by the user. X1 (and X2) have to be defined in the project.
   * start of the subsection: <code>[[Mantel]]</code>   * start of the subsection: <code>[[Mantel]]</code>
-  * size of the matrices (pos. int value): <code>MatrixSize= 5</code> +  * size of the matrices (pos. int value): ''MatrixSize= 5'' 
-  * number of matrices among which we compute the correlations (2/3): <code>MatrixNumber= 2</code> +  * number of matrices among which we compute the correlations (2/3): ''MatrixNumber= 2'' 
-  * matrix that is used as genetic distance ("fst" (->Y=Fst)/ "log_fst" (->Y=log(Fst))/ "slatkinlinearfst" (->Y=Fst/(1-Fst))/ "log_slatkinlinearfst" (->Y=log(Fst/(1-Fst)))/ "nm" (->Y=(1-Fst)/(2 Fst))/ "custom" (->Y= user-specified in the project)): <code>YMatrix = "fst"</code>+  * matrix that is used as genetic distance ("fst" (->Y=Fst)/ "log_fst" (->Y=log(Fst))/ "slatkinlinearfst" (->Y=Fst/(1-Fst))/ "log_slatkinlinearfst" (->Y=log(Fst/(1-Fst)))/ "nm" (->Y=(1-Fst)/(2 Fst))/ "custom" (->Y= user-specified in the project)): ''YMatrix = "fst"''
   * labels that identify the columns of the YMatrix (list containing the names of the lable name belonging to the group, entered within braces):   * labels that identify the columns of the YMatrix (list containing the names of the lable name belonging to the group, entered within braces):
 <code> <code>
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 } }
 </code> </code>
 +
 +
 +===== How to cite =====
 +Excoffier, L. and H.E. L. Lischer (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources. 10: 564-567.
  
  
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