Sequence and Phylogenetic data from "Chlamydial contribution to anaerobic metabolism during eukaryotic evolution"
This dataset is composed of sequence data, alignments, trimmed alignments and tree files for phylogenetic trees presented in this study.
ACK: Acetate kinase
ADI: Arginine deiminase
CK: Carbamate kinase
FeoB: Ferrous iron transporter B subunit
HYDE,F,G: HYDA maturase proteins E,FG
NUOE: HYDC component of trimeric Hydrogenase, and NUOE component of respiratory complex I
NUOF: HYDB component of trimeric Hydrogenase, and NUOF component of respiratory complex I NaH - Na+:H+ antiporter PFO: Pyruvate:ferredoxin oxidoreductase
PTA: Phosphotransaceylase OTC - ornithine transcarbamoylase
Sequence and phylogeny files:
For ACK, ADI, CK, FeoB, HYDA, NUOE, NUOF, NaH, PTA and OTC, there are five files:
unaligned sequences -- *.fasta
tcoffee raw alignment -- *.tcoffee.fasta
masked alignment -- *.tcoffee.bmge.fasta
ultrafast bootstraps tree -- *.uf.treefile
non-parametic bootstraps tree -- *pmsf.treefile
Rogue taxa and transfer bootstrap expectation (TBE) files:
For HYDE, HYDF Family (HYDF_cladeI_cladeII), and HYDF sub-clade (HYDF_cladeI), HYDG and PFO they files are as above but with additional labels distinguishing:
the initial dataset -- *_allTaxa.*
the dataset with rogue taxa removed --*_roguenaroke_removed*
treefile with the the non-parametic bootstrap and TBE values -- *pmsf_tbe.treefile
Ribosomal protein phylogenies:
Concatenated alignments and tree files for phylogenetic trees of ribosomal proteins typically found in an operon (RP15) are included. Contigs from each metagenomic sample encoding at least 5 ribosomal proteins were included in the dataset, alongside a reference dataset of bacterial and archaeal sequences.