This dataset contains protein sequence files and tree files employed in the phylogenetic analysis and molecular dating of the heme-copper oxygen reductases. These ancient enzymes are key components of aerobic respiratory chains and reduce molecular oxygen to water. Heme-copper oxygen reductase sequences were compiled, aligned, and used to construct phylogenetic trees. These phylogenetic trees were coupled with age constraints prior to molecular clock analysis. The resulting molecular clock analyses of these enzymes suggest that they emerged after oxygenic photosynthesis but prior to Earth's Great Oxidation Event. 

The protein sequence files can be viewed as text files, though they alternatively may be opened in a program like Jalview. Tree files may similarly be opened as text files, though a visual representation is possible through a program like FigTree. 

Files in the dataset include:
5360_HCO_Sequence_Alignment_and_Trees.zip
386_HCO_Sequence_Alignment_and_Trees.zip
386_HCO_Sequence_Chronograms.zip

5360_HCO_Sequence_Alignment_and_Trees.zip contains:
Aligned_FFTNS2_5360_Sequence_Set.fasta
Unrooted_Q.pfam_R10_5360_Sequence_Set.treefile
Rooted_Q.pfam_R10_5360_Sequence_Set.figTree

386_HCO_Sequence_Alignment_and_Trees.zip contains:
Aligned_LINSi_386_Sequence_Set.phy
Unrooted_LG_F_I_G4_386_Sequence_Set.treefile
Rooted_LG_F_I_G4_386_Sequence_Set.figTree
Unrooted_LG_F_R10_386_Sequence_Set.treefile
Rooted_LG_F_R10_386_Sequence_Set.figTree

386_HCO_Sequence_Chronograms.zip contains:
CIR_all_topo1_bd_sample.chronogram
CIR_cyanos_topo1_bd_sample.chronogram
CIR_euks_topo1_bd_sample.chronogram
LN_all_topo1_bd_sample.chronogram
LN_cyanos_topo1_bd_sample.chronogram
LN_euks_topo1_bd_sample.chronogram
UGAM_cyanos_topo1_bd_sample.chronogram
UGAM_euks_topo1_bd_sample.chronogram
UGAM_topo1_all_bd_sample.chronogram

CIR_all_topo1_nobd_sample.chronogram
CIR_cyanos_topo1_nobd_sample.chronogram
CIR_euks_topo1_nobd_sample.chronogram
LN_all_topo1_nobd_sample.chronogram
LN_cyanos_topo1_nobd_sample.chronogram
LN_euks_topo1_nobd_sample.chronogram
UGAM_all_topo1_nobd_sample.chronogram
UGAM_cyanos_topo1_nobd_sample.chronogram
UGAM_euks_topo1_nobd_sample.chronogram

CIR_all_topo1_bd_prior_sample.chronogram
CIR_cyanos_topo1_bd_prior_sample.chronogram
CIR_euks_topo1_bd_prior_sample.chronogram
LN_all_topo1_bd_prior_sample.chronogram
LN_cyanos_topo1_bd_prior_sample.chronogram
LN_euks_topo1_bd_prior_sample.chronogram
UGAM_all_topo1_bd_prior_sample.chronogram
UGAM_cyanos_topo1_bd_prior_sample.chronogram
UGAM_euks_topo1_bd_prior_sample.chronogram

CIR_all_topo1_nobd_prior_sample.chronogram
CIR_cyanos_topo1_nobd_prior_sample.chronogram
CIR_euks_topo1_nobd_prior_sample.chronogram
LN_all_topo1_nobd_prior_sample.chronogram
LN_cyanos_topo1_nobd_prior_sample.chronogram
LN_euks_topo1_nobd_prior_sample.chronogram
UGAM_all_topo1_nobd_prior_sample.chronogram
UGAM_cyanos_topo1_nobd_prior_sample.chronogram
UGAM_euks_topo1_nobd_prior_sample.chronogram

CIR_all_topo2_bd_sample.chronogram
CIR_cyanos_topo2_bd_sample.chronogram
CIR_euks_topo2_bd_sample.chronogram
LN_all_topo2_bd_sample.chronogram
LN_cyanos_topo2_bd_sample.chronogram
LN_euks_topo2_bd_sample.chronogram
UGAM_all_topo2_bd_sample.chronogram
UGAM_cyanos_topo2_bd_sample.chronogram
UGAM_euks_topo2_bd_sample.chronogram

CIR_all_topo2_nobd_sample.chronogram
CIR_cyanos_topo2_nobd_sample.chronogram
CIR_euks_topo2_nobd_sample.chronogram
LN_all_topo2_nobd_sample.chronogram
LN_cyanos_topo2_nobd_sample.chronogram
LN_euks_topo2_nobd_sample.chronogram
UGAM_all_topo2_nobd_sample.chronogram
UGAM_cyanos_topo2_nobd_sample.chronogram
UGAM_euks_topo2_nobd_sample.chronogram

CIR_all_topo2_bd_prior_sample.chronogram
CIR_cyanos_topo2_bd_prior_sample.chronogram
CIR_euks_topo2_bd_prior_sample.chronogram
LN_all_topo2_bd_prior_sample.chronogram
LN_cyanos_topo2_bd_prior_sample.chronogram
LN_euks_topo2_bd_prior_sample.chronogram
UGAM_all_topo2_bd_prior_sample.chronogram
UGAM_cyanos_topo2_bd_prior_sample.chronogram
UGAM_euks_topo2_bd_prior_sample.chronogram

CIR_all_topo2_nobd_prior_sample.chronogram
CIR_cyanos_topo2_nobd_prior_sample.chronogram
CIR_euks_topo2_nobd_prior_sample.chronogram
LN_all_topo2_nobd_prior_sample.chronogram
LN_cyanos_topo2_nobd_prior_sample.chronogram
LN_euks_topo2_nobd_prior_sample.chronogram
UGAM_all_topo2_nobd_prior_sample.chronogram
UGAM_cyanos_topo2_nobd_prior_sample.chronogram
UGAM_euks_topo2_nobd_prior_sample.chronogram