Arlequin ver 3.5.1.2

Windows

winarl35.zip	Contains WinArl35.exe, R graphic functions, XML stylescheet and example files.
arlecore_win.zip	Contains 32 bit version of arlecore.exe, as well as a bash script to automatically analyse all arlequin project files present in a given directory. Read the arlecore readme file before using it.
arlsumstat_win.zip	Contains 32 bit version of arlsumstat.exe to compute summary statistics from arlequin projects, a summary statistics definition file, and a bash script to launch it in a Linux environment (you need to install cygwin under windows) . Read the arlsumstat readme file before using it.
Example files_win.zip	Contains examples of arlequin projects.
test_arlsumstat.zip	Example of the usage of arlsumstat to calculate summary statistics from  arlequin projects generated by simcoal3. The bash script test_arlsumstat.sh will call simcoal3 to simulate a sample drawn from a  stationary population and studied at 10 microsatellite loci. Simulated samples will be then analyzed with arlsumstat and output written to a new file.

If you plan to use arlecore or arlsumstat under windows, you will need to dowload cygwinto be able to run Linux bash script under windows. Note that bash scripts are run under windows with cygwin installed by calling the bash command (e.g. bash test_arlsumstat.sh).
Here is also a link on the R-statistical package to download R if you want to be able to generate graphics from Arlequin XML output files.

Linux

arlecore_linux.zip	Contains 32-bit and 64-bit Linux versions of arlecore, the console version of arlequin, as well as a bash script to automatically analyse all arlequin project files present in a given directory. Read the arlecore readme file file before using it.
arlsumstat_linux.zip	Contains 32-bit and 64-bit Linux versions of arlsumstat to compute summary statistics from arlequin projects, a summary statistics definition file, and a bash script to launch it in a Linux environment. Read the arlsumstat readme file before using it.
Example files_linux.zip	Contains examples of arlequin projects. Note that these example files are the same as in the windows version, but that they are translated into the linux text file format.

Here is also a link on the R-statistical package to download R if you want to be able to generate graphics from Arlequin XML output files.

Manuals and readme files

arlequin35.pdf	Contains the latest Arlequin manual (ver 3.5) describing all new routines and graphical outputs
arlecore_readme.txt	Contains a readme file describing the use of arlecore, the console version of Arlequin. This topic is not covered in the Arlequin manual.
alrsumstat_readme.txt	Contains a readme file describing the use of arlsumstat, a specific console version of Arlequin producing summary statistics into a single output file. This topic is not covered in the Arlequin manual.