In this example, we have defined 3 samples consisting of standard multi-locus data with known gametic phase. It means that the alleles listed on the same line constitute a haplotype on a given chromosome. For instance, the genotype G1 is made up of the two following haplotypes: AD on one chromosome and BC on the second, A and b being two alleles at the first locus, and C and D being two alleles at the second locus. Note that the same allele identifier can be used in different loci. This is obviously true for Dna
sequences, but it also holds for all other data types.
[Profile]
Title="An example of genotypic data with known gametic phase" NbSamples=3
GenotypicData=1 GameticPhase=1
#There is no recessive allele RecessiveData=0 DataType=STANDARD LocusSeparator=WHITESPACE [Data] [[Samples]] SampleName="standard_pop1" SampleSize=20 SampleData= { G1 4 A D B C G2 5 A B A A G3 3 B B B A G4 8 D C D C } SampleName="standard_pop2" SampleSize=10 SampleData= { G5 5 A C C B G6 5 B C D B } SampleName="standard_pop3" SampleSize=15
Manual Arlequin ver 3.5.2 Examples of input files 50 SampleData= { G7 3 A D C A G8 12 A C B B } [[Structure]] StructureName="Two groups" NbGroups=2 Group={ "standard_pop1" } Group={ "standard_pop2" "standard_pop3"
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6 ARLEQUIN INTERFACE
The interface of Arlequin (since ver. 3.0) is written in C++ and looks like:
The graphical interface is made up of a series of tabbed dialog boxes, whose content vary dynamically depending on the type of data currently analyzed.
6.1 Menus
6.1.1 File Menu
New project... Prompts the Project Wizard dialog box Open project... Opens a dialog box to locate an
existing project
Close project Closes the current project.
Recent projects… Open a submenu with the last 10 more recently opened projects Load settings... Load previously saved computation
settings
Save settings Save current computation settings Save settings as ... Save current computation settings
under a specific name
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6.1.2 View Menu
Project information Open tab dialog with information on current project
Settings Open specific tab dialogs to active some computations and choose their associated settings
View Project View current project in text editor
View Results View computation result in default web browser View Log file View log file in text editor
Show button text Toggle presence/absence of text associated to toolbar buttons
6.1.3 Options Menu
Use 64bit external arlecore program for computations
Check this menu item if you want Arlequin to use the program arlecore64.exe to perform computations of the selected options, instead of WinArl35 itself. The
advantage is that arlecore64.exe is a 64 bit program, which can handle larger data sets, and which is more optimized than WinArl35.exe, and thus computations will be faster.
XML Output Check this menu item if you want Arlequin to generate output files in xml format, allowing for more flexibility in the formatting of the output, and the inclusion of
graphics generated by an R script (see section 7.8). If this menu is unchecked, conventional html files are
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generated, and graphs cannot be incorporated into output files.
Append results If checked, Add results of a new analysis at the end of the current result file. Otherwise, previous results are deleted before adding the new results.
Use associated settings Check this box if you want Arlequin to automatically load the settings associated to each project. If this box is unchecked, the same settings will be used for different projects (see section 6.3.2).
Keep Amova null distributions If checked, the null distribution of variance components are written in specific files (see section 6.3.2).
Prompt for handling unphased multi-locus data
If checked, you will have the option of estimating the gametic phase of unphased genotype data with the ELB algorithm (see section 6.3.8.4.2.1).
6.1.4 Help Menu
The menu to get access to the Help File System
Arlequin PDF Help file Open Arlequin help file. Actually it tries to open the file "arlequin.pdf". You thus need to have installed the Adobe Acrobat extensions in your web browser.
Arlequin web site Link to Arlequin web site
http://cmpg.unibe.ch/software/arlequin3"
R project Link to the R project web page http://www.r-project.org/
R is a language and environment for statistical computing and graphics, that needs to be installed on your computer to include graphs in output files
About Arlequin… Some information about Arlequin, its authors, contact address and the Swiss NSF grants that supported its development.
6.2 Toolbar
Arlequin’s toolbar contains icons that are shortcuts to some commonly used menu items as shown below. Clicking on one of these icons is equivalent to activating the
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The individual buttons perform the following actions:
Opens a dialog box to choose an Arlequin project to open (see section 6.3.1)
Calls the text editorspecified in the Arlequin Configuration tab (see section6.3.3) and loads the current Arlequin project, allowing you to edit it.
View results in your web browser
View Arlequin log file in the selected text editor
Closes the current project
Calls R routines to integrate graphics of results into the xml output file
Start currently selected computations
Pauses current computations
Stops current computations