creating bash script to automate task for analyzing multiple files
<p>I don't have a lot of experience with scripting.</p>

<p>I have a directory that contains, among many other files, a set of <code>*.phylip</code> files I need to analyze with a program. I would like to automate this task. I think a loop bash shell script would be appropriate, although I could be wrong.</p>

<p>If I was to perform the analysis manually on one <code>.phylip</code> file, I would use the following command in terminal:</p>

<pre><code>./raxmlHPC-SSE3 -m GTRCAT -y -s uce-5.phylip --print-identical-sequences -p 12345 -n uce-5_result
</code></pre>

<p>For the bash shell script, I think it would be close to:</p>

<pre><code>#!/bin/sh
for i in $( ls ); do
    ./raxmlHPC-SSE3 -m GTRCAT -y -s uce-5.phylip --print-identical-sequences -p 12345 -n test_5 $i
done
</code></pre>

<p>The issue I'm aware of, but don't know how to fix, is the -s option, which specifies the input phylip file. Any suggestions on how to modify the script to do what I need done?</p>