deletions | additions       diff --git a/Methods.md b/Methods.md  index cd60d9e..1b44553 100644  --- a/Methods.md  +++ b/Methods.md 
...
Genomic DNA was extracted using a Wizard Genomic DNA Purification Kit (Promega). A nearly full-length 16S rRNA gene sequence was amplified using the 27F (5'-AGAGTTTGATCMTGGCTCAG-3') and 1391R (5'-GACGGGCGGTGTGTRCA-3') "universal" primers. Sanger sequencing was provided by the College of Biological Science UC-DNA Sequencing Facility (UC Davis). This DNA was also used for Illumina sequencing of the draft genome as described elsewhere (Coil and Eisen, in press). The genome sequence was annotated using the RAST server \cite{Aziz_2008} \cite{Overbeek_2013}.  The 1482bp 16S rDNA sequence was obtained from the genome assembly in RAST (GenBank: KP122961.1), and uploaded to the Ribosomal Database Project (RDP) \cite{Cole_2013}. Since the RDP database is incomplete with respect to the _Erythrobacteraceae_ family, additional type strain sequences were obtained from NCBI to ensure that every member of the family with official standing in nomenclature ([http://www.bacterio.net/](http://www.bacterio.net/) ([http://www.bacterio.net/](http://www.bacterio.net/))  was present in the alignment downloaded from RDP. Because the taxon names exported with this alignment contained special characters that were not compatible with phylogenetic reconstruction software, a custom script was used to remove or replace those characters with underscores. A description of and link to this script can be found in \cite{26020012}. This alignment was used to generate a variety of phylogenetic trees including Maximum Likelihood (RaxML, \cite{24451623}), Bayseian (MrBayes, \cite{12912839} \cite{11524383}), Neighbor-Joining (MEGA6, \cite{24132122} and NINJA, [http://nimbletwist.com/software/ninja/](http://nimbletwist.com/software/ninja/), and Maximum Parsimony (MEGA6). The alignment was manually examined using MView ([http://www.ebi.ac.uk/Tools/msa/mview/t](http://www.ebi.ac.uk/Tools/msa/mview/), the secondary structure was generated using the RNAfold Web Server ([http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi](http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) and visualized with Forna ([http://nibiru.tbi.univie.ac.at/forna/](http://nibiru.tbi.univie.ac.at/forna/). Dendroscope 3 \cite{22780991} and FigTree ([http://tree.bio.ed.ac.uk/software/figtree/](http://tree.bio.ed.ac.uk/software/figtree/) were used to view and edit the phylogenetic trees.