Q: fastDNAml for DOS/Windows (compiling problem)?
aeb25 at uni-koeln.de
Thu Feb 18 06:51:23 EST 1999
Joern Hopke <jhopke at u.washington.edu> wrote:
> execute the program, getting the following output:
> fastDNAml, version 1.1.1a, November 2, 1994
> Based on Joseph Felsenstein's
> Nucleic acid sequence Maximum Likelihood method, version 3.3
I am not familiar in doing this under Windows, but I can tell you roughly,
how it works under a Unix environment.
> and a blinking cursor. Assuming, an input-filename was required, I
> entered test5.phy (from the RDP site + I tried it with one of my own
> files), but came up with the following error message:
> ERROR: Problem reading number of species and sites
Under Unix I usually start fastDNAml with the following command line:
nohup fastDNAml <input_file.phy> fast.out &
nohup shouldn't have a meaning for you. It simply tells the system that it
shouldn't stop running, when the user logs out. The "&" makes the programm
running in the background, which is (possibliy) as well Unix stuff.
For the rest:
fastDNAml <input_file.phy> fast.out
fastDNAml = start the program
<input_file.phy = feed it with the input file input_file.phy
> fast.out = save the output of the analyses in a file called fast.out (sure
you can choose the name)
I don't know how this feeding in and out is handled in DOS commands.
Possibly you need other signs than < and >.
> I guess, the input file format should be correct (since it's a sample
> file from the RDP site and it looked all right when viewing it in an
> editor), so, probably during the compilation something went wrong
> (though no error message was generated by the compiler - I didn't try
> all that with the DNArates program).
There is another thing to be aware of: In the Phylip package you are offered
a menu after starting the program, in which you can choose between different
In fastDNAml, you either take the scripts the program comes with, but those
are for Unix shells, or you load the phylip file in a text editor to write
the options you want in the top line.
It should start with the number of taxa and the number of sites (already
coming with the phylip format) then you add e.g. G O Y J.
It should look something like this:
12 390 G O Y J
[the list of data starts here]
G = global rearrangements
O = outgroup present and defined in next line as taxon number 3
J = do jumbling and defined in third line as seed 7
Y = print out tree to file
I can't tell you whether it works under Windows. But if you need this
program badly, you still have the option to put another harddisk in the PC
or sacrifice one partition of your already existing harddisk and install a
small linux system on it (or perhaps your find somebody to do this for you).
I have fastDNAml running under linux and it works fine.
kerstin.hoef-emden at uni-koeln.de
kerstinh at bot.ku.dk
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