Description
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). (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). (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.