Giving options to Command line Clustalw

Question

[Jacob]

I am trying to run the command line clustalw, but within a loop. Because of this I want to be able to set all the parameters at the time of execution, I don't want to change the parameters manually while the program is running Here is what I am running

clustalw
1. Sequence Input From Disc
Enter the name of the sequence file: file.txt
2. Multiple Alignments
     9. Output format options
          "4. PHYLIP format output" to "ON"
     1.  Do complete multiple alignment now (Slow/Accurate)

I would like to run this as one command on the command. This is about as much as I can come up with because I can't seem to find the other options here

clustalw -INFILE=file.txt

Answer 1

[Jacob]

clustalw < input.txt

Where input.txt is

1
file.txt
2
9
4
^@
1
^@
^@
^@
X
^@
X

The ^@ is one character, not two. It works as the enter key. You can type it like this

1. vim input.txt
2. i #going into insertion mode within vim
3. CTRL + v 
4. CTRL + j #Alternatively CTRL + the enter key

Answer 2

[Mirko]

./clustalw -INFILE=file.ext -OUTPUT=PHYLIP should do.