How To Run Phylip Dnadist In A Highthroughput Way?

Question

[cacaucenturion]

Hi all,

I want to run phylip dnadist but not with the interacting interactive way where I have to modify the parameters and input 'Y' frequently. How can I use it more conveniently? Thanks!

Answer 1

[Neilfws]

From the Phylip FAQ - "Why didn't it occur to you to allow the options to be set on the command line?"

You may be asking this question because you want to automate the operation of PHYLIP programs using batch files (command files) to run in background. If that is the issue, see the section of this main documentation page on "Running the programs in background or under control of a command file".

Here is the main documentation page. Here is the appropriate section.

Answer 2

[Hamish]

While PHYLIP supports this via command-scripts (see the other answers for ways of dealing with this), command-line support can be found in the EMBOSS EMBASSY package PHYLIPNEW.

If you are using a Debian based Linux distribution this can be installed via the embassy-phylip package (my be installed by the med-bio and science-biology meta-packages). Other distributions may also have ports, or you can always build from source (see "Downloading EMBOSS").

For details of the 'fdnadist' program (which is equivalent to PHYLIP's 'dnadist') see: http://emboss.sourceforge.net/apps/release/6.0/embassy/phylipnew/fdnadist.html

Answer 3

[Pawel Szczesny]

The general way of automated running of an interactive software is to open a process as a filehandle and print directly to it. For example, in Perl it would be:

open (FH, "interactive_program|"); #notice the "|" 
print FH "some\n";
print FH "control\n";
print FH "Y\n";
close (FH);

That way you can automate PHYLIP or something else.