Supplementary Data for Farrell, Nesbø and Zhaxybayeva (2023)

16SrRNA TreesandPuzzle.zip:
16SrRNA_describedSpecies_trimmed.aln: 16S rRNA gene alignment for described Thermotogota species, trimmed; used in likelihood mapping analyses presented in the Supplementary Figures 2A and 2B

16SrRNA_describedSpecies_iqtreeX2Heterogeneity.txt: Text file of X^2 test of heterogeneity for the described Thermotogota species alignment

16Sr16SrRNA_withClones.aln: 16S rRNA gene alignment with environmental sequences included; used for trees in Supplementary Figures 1A and 1B.

16SrRNA_withclones.tree: Tree in Newick format for Supplementary Figure 1A

16SrRNA_withclones_iqtreeX2Heterogeneity.txt: Text file of X^2 test of heterogeneity for tree with environmental sequences as shown in Supplementary Figure 1A

16SrRNA_clones_nhPhymlEq.tree: Tree in Newick format for Supplementary Figure 1B

Ribosomal_Proteins_Analyses.zip:
concat_rprotTree_DescribedSpeciesStrains.aln: Concatenated alignment of 50 ribosomal proteins from described Thermotogota species; used for tree in Supplementary Figure 3

concat_rprotTree_DescribedSpeciesStrains.tree: Tree in Newick format for Supplementary Figure 3

concat_rprot_withMAGs.aln: Concatenated alignment of 50 ribosomal proteins from Thermotogota described species and MAGs; used for tree in Supplementary Figure 4

concat_rprot_withMAGs.tree: Tree in Newick format for Supplementary Figure 4

individual_Rprot_alignments.zip: Alignment and Tree-Puzzle output file for each of the 50 ribosomal proteins 

Single_Copy_Core_Protein_Analyses.zip:
CvP_IVYWREL_plots.py: Script used to compare IVYWREL bias to OGT for all genomes after removing transmembrane proteins

concat232SCC.trimaln: Concatenated and trimmed alignment file for the 232 single-copy-core proteins used in all SCC analyses.

concat232SCC.tree: Tree in Newick format reconstructed under a homogenous model; shown on Figure 1

concat232SCC.tree.log: IQ-Tree output log for the SCC tree shown on Figure 1

concat232SCC.trimmedalignment.customDayhoffRecoding.phy: Alignment in Phylip format after recoding using custom-Dayhoff bins

concat232SCC.customDayhoffRecoding.RAxML.tree: Tree in Newick format reconstructed from the custom recoded alignment; shown on Supplementary Figure 7

concat232SCC.PSMF.tree: Tree in Newick format reconstructed under PSMF Model; shown on Supplementary Figure 8

concat232SCC.GHOST.tree: Tree in Newick format reconstructed under GHOST Model; shown on Supplementary Figure 9

recode_sequences.py: Script used for recoding alignment files

Gene_Family_Minimum_Bipartition_Analyses.zip
compute_MinimumBipartitionsData_fromTrees.py: Script used to compute the minimum bipartitions data from phylogenetic trees

named_trees.zip: Newick-formated trees (leaves with accessions and leaves with names) for orthogroups containing Mesoaciditoga lauensis. 

Orthogroup_Sequences.zip: Amino acid sequences of proteins (in FASTA format) for all orthogroups detected in analyzed Thermotogota genomes; only orthogroups including both A. saccharophila and M. lauensis were used in minimum bipartition analyses.

STRING_files.zip
Network_A folder: Network on Panel A of Figure 5

string_functional_annotations.tsv: Functional annotations for each node, including "STRING cluster" categories

string_interactions.tsv: Node interaction information, including interaction strength

string_mapping.tsv: Map of gene accessions to STRING gene identifiers

string_normal_image.png: Image of STRING network before it was edited for Figure 5

Network_B folder: Network on Panel B of Figure 5

string_functional_annotations.tsv: Functional annotations for each node, including "STRING cluster" categories

string_interactions.tsv: Node interaction information, including interaction strength

string_normal_image.png: Image of STRING network before it was edited for Figure 5