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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.


Protein abbreviations:

ACK: Acetate kinase

ADI: Arginine deiminase

CK: Carbamate kinase

FeoB: Ferrous iron transporter B subunit

HYDA: [FeFe]-Hydrogenase

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.


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