deletions | additions       diff --git a/Methods.md b/Methods.md  index 4dea476..06fc06f 100644  --- a/Methods.md  +++ b/Methods.md 
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Cells were grown to post exponential phase (~72 hours) in 1L of LB at 23°C for large-scale biomass production, then centrifuged and lyopholized. Analysis of respiratory quinones/polar lipids and fatty acids were carried out by the Identification Service, DSMZ, Braunschweig. Germany. Protocol details and references can be found at the following DSMZ pages; [polar lipids](https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-polar-lipids.html), [respiratory quinones](https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-respiratory-quinones.html), [cellular fatty acids](https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-cellular-fatty-acids.html).  **16S rDNA and Genome Sequencing**  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, submitted). The genome sequence was annotated using the RAST server \cite{Aziz_2008} \cite{Overbeek_2013}.  A phylogentic tree was inferred using all type strains from the _Erythrobacteraceae_ family. 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 was used database is incomplete with respect  tobuild an alignment including every type strain within  the _Erythrobacteraceae_ family, including additional type  strain Coronado(T). 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/) 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).  This alignment was used to generate DISCUSS ALL TREES HERE  
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FastTree \cite{19377059} was used with default settings to build an unrooted phylogeny. Dendroscope 3 \cite{22780991} was used to view and edit the phylogenetic tree in order to 1) root the tree with a clade that is sister to a well-supported clade containing strain Coronado(T), 2) prune the tree to remove taxa outside the clade containg the outgroup, and 3) "clean up" the tree.