Last change: 12.March.2020

# This directory contains files used for recruiting NCLDV PolB marker genes from the OM-RGC.v2.
# The resulting files of hhmmsearch and pplacer are also included.

Existing files:

# Files for hmmsearch
NCLDV_PolB.hmm: HMM profile of NCLDV PolBs used for hmmsearch.
hmmsearch_result.fasta: Result of hmmsearch against OM-RGC.v2

# Files for pplacer
pplacer_ref211.msa: Multiple alignments of the PolB reference sequences for pplacer analysis.
RAxML_result.pplacer.nwk: Phylogenetic tree constructed from the reference sequences.
RAxML_info.pplacer.txt: Information on the reference phylogenetic tree.
pplacer_result.jplace: Results of pplacer phylogenetic placement.
NCLDV_PolB_6818.faa: Amino acid sequences of NCLDV PolBs detected using pplacer.


Reference:
Hisashi Endo, Romain Blanc-Mathieu, Yanze Li, Guillem Salazar, Nicolas Henry, Karine Labadie, Colomban de Vargas,
Matthew B. Sullivan, Chris Bowler, Patrick Wincker, Lee Karp-Boss, Shinichi Sunagawa, Hiroyuki Ogata*
Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions
(manuscript submitted)

If any question please contact: endo@scl.kyoto-u.ac.jp