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The resulting datasets were analyzed using custom software with a graphical user interface, and plots of residue properties or abundance can be generated at http://www.tmdsonline.org.org

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The NCBI taxonomic classification tree was generated at http://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi (July 14 , 2014 based on the taxonomic identifiers for the species of the QfO reference proteomes.

Gene-expression profiles from the two data sets were compared by ranking genes measured in the two experiments according to their signed log10 p-value of differential expression between class A and class B. RRHO heat maps that graphically and statistically visualize correlations between two expression profiles were generated at http://systems.crump.ucla.edu/rankrank/ [ 23].

The alligator and turtle BES reads were generated at The Institute for Genomic Research, Rockville, MD http://www.tigr.org and the emu BESs at the Broad Institute, Cambridge, MA http://www.broad.mit.edu using published protocols [ 2, 27].

The species tree was generated at NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi).nih.gov/Taxonomy/CommonTree/wwwcmt.cgi

SUP05 SAGs were generated at the Bigelow Laboratory for Ocean Sciences (http://scgc.bigelow.org, [ Stepanauskas and Sieracki, 2007; Swan et al., 2013]).

Taxonomic binning of classified sequences was generated at five levels, from phylum to genus (http://metadp.cn:7001/metadp/F2/barchart_for_samples.html).html

The minimum number of motif occurrences was also lowered and was set to 5. Sequence logos were generated with Weblogo at http://weblogo.berkeley.edu [45].

The sequence logos were generated online at logo platform (http://weblogo.berkeley.edu/).edu/

An example dataset was generated using PopSim, available at http://www-personal.une.edu.au/~bkinghor/genup.htm.edu.au/~bkinghor/genup.htm

Sequences for the DNA template used for in vitro transcription of the RNA probe were generated with primer sets available at http://www.genepaint.org.org

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