Supplementary Data

(1) recA data: recA.tgz

recA.tgz contains the following files:
recA_GOS.pep ------------------ Amino acid sequences for GOS RecAs 
recA_ref.pep ------------------ Amino acid sequences for RecAs from NRAA and genome sequences 
recA_cluster.txt -------------- Lek clusters of RecA sequences (Table 1)
recA.ali ---------------------- Original alignment for the RecA tree (Figure 1) 
recA.trim.ali ----------------- Trimmed RecA alignment that the RecA tree is built upon (Figure 1)
recA.tre ---------------------- RecA tree in Newick format (Figure 1)
recA_GOS_pepID_assemblyID.map - The assembly IDs of the recA encoding GOS assemblies (Table 2) 
recA_linked.pep --------------- The Amino Acid sequences of the genes that share assemblies with the GOS novel recA (Table 2)  
recA.novel.cDNA --------------- The DNA sequences of novel recA genes

(2) rpoB data: rpoB.tgz

rpoB.tgz contains the following files:
rpoB_GOS.pep ------------------- Amino acid sequences for GOS RpoBs 
rpoB_ref.pep ------------------- Amino acid sequences for RpoBs from NRAA and genome sequences 
rpoB_cluster.txt --------------- Lek clusters of RpoB sequences (Table 3)
rpoB.tre.ali ------------------- Original alignment for the RpoB tree (Figure 3) 
rpoB.tre.trim ------------------ Trimmed RpoB alignment that the RpoB tree is built upon (Figure 3)
rpoB.tre ----------------------- RpoB tree in Newick format (Figure 3)
rpoB.novel.cNDA ---------------- The DNA sequences of novel rpoB genes

(3) ss-rRNA data: ssu.tgz

ssu.tgz contains the following files:
SSU_GOSreads.fa ---------------- GOS ss-rRNA sequences    
SSU_GOSreads_deepbrach.fa ------ Potential GOS deep-branching ss-rRNA 


(4) Lek Clustering Program: lek.tgz

lek.tgz contains scripts for the Lek clustering protocol. 
Instructions can be found in the included README file.