Internalizing archaea: a paradigm shift

Repository contents

1_Phylogenies.tar.gz includes all files needed to generate the phylogeny shown in Figure 4 of the associated manuscript. Specifically, this includes: 

The Workflow used to generated the species tree

Any required dependencies such as custom scripts or custom databases

The protein files from 

The proteins from all archaeal reference genomes that were used to generate the protein tree

The 51 marker proteins used to generate the species tree

The mafft_linsi alignments of the 51 marker proteins

The BMGE trimmed alignments of the 51 marker proteins

The concatenated alignment used to generate the species tree

The output of the IQ-TREE analysis

2_Protein_search.tar.gz includes all files needed to generate (a) the HMM profiles specific the two proteins with a coiled-coil protein (CCP) domain (referred to as Locus1 and Locus2 throughout the description) and (b) the Phyre2 results for all potential Locus1 and Locus2 proteins found in the archaea reference set. Specifically, this includes:

(a)

 The script used to build the HMM profiles

Any required dependencies

The sequences of Locus1 and Locus2 proteins, including the individual proteins, the aligned proteins and the trimmed alignments.

All HHsearch results

The HMM profiles

(b)

The results for the batch search run for all potential Locus 1 and Locus2 proteins found across DPANN archaea

The results for the sensitive search run for the Locus1 and Locus2 proteins from Cand. N. antarcticus

3_Orthogroup_Data.tar.gz includes all files relating to groups of orthologous proteins generated by OrthoFinder. Specifically this includes:

List of assemblies included in the analysis

List of the number of proteins belonging to each orthogroup for each genome in the analysis.

List of each orthogroup and the identifiers for each protein in each genome that were assigned to that orthogroup.

List of the protein IDs for every protein in each orthogroup. Does not contain genome information.

List of how many orthogroups are shared between each genome

List of genes from each genome not assigned to an orthogroup

Distribution of orthogroups across major phyla.

General statistics for the orthogroups

General statistic for each genome