Software recommendations - DNA composition
There are more R packages available that calculate GC content, for example Ape's GC.content() function.

For example:

&gt; library(ape)
&gt; data(woodmouse)
&gt; GC.content(woodmouse)
[1] 0.3873347


With a sliding window is in Biostrings package.

&gt; library(Biostrings) 
&gt; DNA &lt;- DNAString("ACTGAAACCGTGGCAGTTTGAC")
&gt; letterFrequencyInSlidingView(DNA, view.width=4,letters="CG")


For codon usage bias, I think cubfits or sscu packages might be useful.