Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes
Dongying Wu, Martin Wu, Aaron Halpern, Doug Rusch, Shibu Yooseph, Marvin Frazier, J. Craig Venter, Jonathan A. Eisen

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.