Dear all,

First of all thanks a lot for the responses I had to my question about 
user-friendly population genetics programs that run in Mac OSX. 
Unfortunately, there doesn't seem to exist such a programme with a 
graphical interface, which I find curious given that Macs used to be 
more user-friendly than Windows. Here I post the answsers I have had.

Cheers,

Ramiro

1) What about running DnaSP/DAMBE/etc. on Windows (with bootcamp or 
Parallels) on the Mac instead?

2) Given your post on the Evoldir, I cannot help but plug my own 
software, GenoDive. However, it does not handle sequences, but it does 
handle most other types of genetic markers and can perform several 
different analyses with them, among which AMOVA's. Anyway, as far as I 
can tell myself it is very user friendly, and may be useful to you for 
some other purposes. The current version can be downloaded from my 
website: http://www.bentleydrummer.nl/software. Please keep in mind 
that it is a beta version, so there may still be some bugs.

3) The package of software written by Kevin Thornton and Eli Stahl 
(molpopgen) is excellent and very flexible. This package is written in 
C++, and it was relatively painless to compile on my Mac (which runs  
OSX Tiger). In particular, the 'analysis' package can do most of the 
analyses that DnaSP can do.

4) I saw your post of Evoldir.   There is nothing that I am aware of in 
terms of software with a graphical interface.  On Intel-based macs, you 
can run DNAsp through one of the many windows emulators available 
(Parallels, VMware, etc.). Alternatively, I have written several 
software packages of command-line applications which are portable 
across many Unix systems, and work fine on OS X.  
http://www.molpopgen.org

5) Kevin Thornton has a set of applications (MKtest, compute, polydNdS) 
for this sort of thing that work well on Mac OSX; they are available at 
molpopgen.org. They are not as user-friendly as DnaSP - you have to run 
them from the terminal, and you will need to compile them from C++ 
source code (after downloading and installing libraries - instructions 
are on the website too).

6) You could try GenAlEx6 or Genepop 4.0.

7) You can use Jeffrey Townsend's SeqPop that runs command-line on the 
terminal: http://www.yale.edu/townsend/software.html

A similar option is Kevin Thornton's collection of command-line 
programs that use his libsequence library: 
http://molpopgen.org/software/lseqsoftware.html

A nice Java program is Fu & Li's NeutralityTest: 
http://www.hgc.sph.uth.tmc.edu/neutrality_test  It implements a variety 
of tests, like Fu's, Fu & Li's, Tajima's, Fay & Wu's, MK, HKA, LWL, 
Suzuki-Gojobori.

There a way to run Windows programs without installing Windows per se. 
The application is called WINE and exists for Linux. It was recently 
ported to OSX. There is the DarWINE project, but the current version is 
for PowerPC (PPC) architecture, not Intel-based Macs. This requires 
getting your hands dirty and installing libraries, compiling, etc. A 
company called CodeWeavers (http://www.codeweavers.com/products/cxmac) 
are selling CrossOver for the Mac and Linux, so as to run Windows 
applications seemlessly. The academic price is $42 and DnaSP runs just 
fine.

If you have long sequences, like genomic data, the DnaSP crew has 
written VariScan: http://www.ub.es/softevol/variscan

If you're interested in simulations and test statistics, Sebas 
Ramos-Onsins from the Univ. of Barcelona has written mlSimCoal (based 
on Hudson's famous ms program): http://www.ub.es/softevol/mlcoalsim

Peter Andolfatto from UCSD has a few programs like that at 
http://www-biology.ucsd.edu/labs/andolfatto/Programs.html

8) Have you tried Arlequin ( lgb.unige.ch/arlequin/ )? Although I 
haven't used the Mac version, they do have one and it does alot of 
tests, including neutrality. Once you get your dataset into the proper 
format (GenePop on the web can do this for you), which is a pain, it's 
fairly user friendly.

Dr. Ramiro Morales-Hojas
Molecular Evolution Lab
IBMC
Rua do Campo Alegre 823
Porto
4150-180
Portugal

e-mail: rmhojas@ibmc.up.pt

rmhojas@ibmc.up.pt