March 2024 Needed softwares for the training course of T.

De Meeûs
empirical population genetics for beginners

List of softwares that will be needed for the population genetics training course, with
links for downloading and references when available. Make sure that these are
installed and work properly before the training course begins.

Please read this document entirely and carefully

For an optimal use of these softwares please download each of those in a particular folder
(e.g. BAPS) in your hard drive (e.g. C or D). For instance, I downloaded BAPS in D:\BAPS. Then,
when required, unzip the files needed in the same folder. Sometimes, zipped files contain other zipped
files (e.g. Genepop). In that case, choose the files you need and unzip those (in the same folder, e.g.
exe.zip for Genepop and then Win64.zip if your processor is 64 bits). Some executables or softwares
require the processor being identified (32 or 64 bits). If you do not know it, open your Windows
explorer, just right click on "This PC" or "My Computer" or any other name of that sort and click on
"Properties". A frame will appear giving you the information.
To handle data, we will make much use of a table spreadsheet software such as Microsoft
Excel or its free version "OpenOffice Calc" (http://www.openoffice.org/). We may also need a graphic
editor as Open Office Draw (or PowerPoint).
It is important that you do not copy these softwares on the desktop of your computer and
launch those from there. Each software needs being copied in a hard folder.
It will be very useful that you see file extensions. In Windows, this may be easily achieved with
the Windows' file explorer. On the top of the frame of Windows file explorer click on the tab "view" or
"Screen display" and tick the box "File extensions" or "File extension names" or "Extension of file
names".
It is important that you know how to type "\" and "#".

All other softwares that we will or may need are listed in Table 1 (see below).

If your version of Windows seems incompatible with a software, it may sometimes be simply
fixed by just right clicking on the executable, go to "properties" and specify the software must be
launched as XP compatible. You may also need to set yourself as the superuser or manager of your
computer.

For Mac users you may install Wine from https://www.winehq.org/

Finally, you may find useful files in my web site at http://t-de-meeus.fr/EnseignMeeus.html, in

particular tutorials and a pdf version of my book (1st edition in French) at
http://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers14-01/010058052.pdf.
March 2024 Needed softwares for the training course of T. De Meeûs
empirical population genetics for beginners

Please read this document entirely

Table 1: Needed softwares

Software URL Authors and dates Ref.

Corander & Marttinen

BAPS (a) http://t-de-meeus.fr/ProgMeeusGB.html (1,2)
(2005)

Bottleneck http://www1.montpellier.inra.fr/CBGP/software/Bottleneck/ Piry et al. (1999) (3,4)

Colony https://www.zsl.org/science/software/colony Jones & Wang (2010) (5,6)

Convert http://t-de-meeus.fr/ProgMeeusGB.html Glaubitz (2004) (7)

CREATE http://t-de-meeus.fr/ProgMeeusGB.html Coombs et al. (2008) (8)

Estim http://t-de-meeus.fr/ProgMeeusGB.html Vitalis (2001) (9,10)

Chapuis & Estoup

FreeNA http://www1.montpellier.inra.fr/CBGP/software/FreeNA/ (11)
(2007)

Fstat 2.9.4 http://t-de-meeus.fr/ProgMeeusGB.html Goudet (2003) (12)

Genepop 4 http://kimura.univ-montp2.fr/~rousset/Genepop.htm Rousset (2008) (13)

Genetix (b) https://kimura.univ-montp2.fr/genetix/ Belkhir et al (2004) NA

http://www.molecularfisherieslaboratory.com.au/neestimator-
NeEstimator (c) Do et al (2014) (14)
software

MEGA https://megasoftware.net/ Kumar et al (2017) (15)

MultiTest V.1.2 http://t-de-meeus.fr/ProgMeeusGB.html De Meeûs et al. (2009) (16)

PopTree (d) http://www.kms.ac.jp/~genomelb/takezaki/poptree2/index.html Takezaki et al. (2010) (17)

R Development Core
R (e) http://www.R-project.org NA
Team (2013)

RecodeData https://patrickmeirmans.com/software/Other%20Software.html Meirmans (2006) (18)

https://web.stanford.edu/group/pritchardlab/structure_software/releas
Structure Pritchard et al 2010 (19)
e_versions/v2.3.4/html/structure.html

Structure Selector (f) https://lmme.ac.cn/StructureSelector/ Li & Liu (2018)(20) (20,21)

Text Pad (g) https://textpad.com/download/index.html NA

(a) BAPS. The official website does not work anymore. If you want the last version ask directly to
Jukka Corander <jukka.corander@medisin.uio.no>.
March 2024 Needed softwares for the training course of T. De Meeûs
empirical population genetics for beginners

(b) In French, but very easy to use, with useful utilities. The help menu does not work anymore on
newest versions of Windows, but it can be accessed on line at https://kimura.univ-
montp2.fr/genetix/.

(c) For NeEstimator, the best interface is for Java. You thus need to have Java installed on your
machine (search for Java in the net and install it, it is free). Then the program is launched by
double clicking on NeEstimator2x1.jar.

(d) The computation of the tree and bootstraps will not work in most European Windows interface. To
make it work, you will need to configure your computer setting with "." as the decimal sign. To
do that, you need to click on the magnifying glass (bottom right of the screen) and type
"Configuration panel" and "Enter". Click on "Region" (planet earth with a clock). Then click on
"Supplementary parameters". In "Decimal symbol" choose "." and click on "OK". Then,
PopTree should work fine.

(e) with packages Rcmdr (R-Commander) (22,23), ADEGenet (24), geosphere (25) and HierFstat
(26,27). If these packages are not already installed in your machine, you will need to uninstall
R and install the latest version of it. Once you have installed R, then launch R. For HierFstat,
please see below. In the menu "Packages" choose "Install packages" and then choose the
nearest CRAN mirror (e.g. Lyon 1). In that mirror, you will look for the requested package and
select it. Then this should be OK. To test if the package is correctly installed go to the
"Packages" menu and select ""charge" or "launch" "package" and select the package you
want to test (e.g. Rcmdr). If it is ok then you will see a frame "R Commander" appear, after a
few seconds (please be patient). Otherwise, it will tell that some other packages are missing.
Say "yes" if the menu propose to install those, or note the names of these missing utilities and
go back to the "install package" menu to look for those and install them.
At first launch, Rcmdr may take some time to appear as a new frame. Just be patient.
I have written a tutorial in French available at http://t-de-meeus.fr/EnseignMeeus.html.
Important notice for HierFstat. The site for updating hierfstat can be found at
https://github.com/jgx65/hierfstat. in R, choose the mirror of CRAN where you want to be
(menu "Packages-choose a CRAN mirror"). Install packages devtools, ADE4 and ADE-Genet
with the menu "Packages-Install package". You also need to install RTools, from the self-
installing executable to be downloaded at https://cran.r-project.org/ in "R Binaries". Then, in
the R console type:

library(devtools)
install_github("jgx65/hierfstat")
library("hierfstat")

To verify you get the correct version type:

sessionInfo()

This should do. If not, then you may need to totally uninstall all R versions from your computer. Delete
all residual files, in particular those in Program folder and in Documents folder that concern R.
Then reinstall R and repeat the process to install HierFstat as described above.

(f) This is just a link to an online facility. There is no need to download anything here, just to check you
can access to it.

(g) Or any other text editor that can handle blocks and find-replace special characters such as tabs
and carriage returns, if you feel more comfortable with it. Please, for the sake of homogeneity
among every attendants, download the English version of the software.

It is important that you test that these softwares and packages work on your machine,
otherwise it will take some time during the training course to solve eventual problems so that
everybody can follow.

In case of problems, please send me an e-mail. Do not wait until the training course has
begun.
March 2024 Needed softwares for the training course of T. De Meeûs
empirical population genetics for beginners

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