Analysis scripts and supplementary data for Gortzia yakutica paper.
Beliavskaia AY, Predeus AV, Garushyants SK, Logacheva MD, Gong J, Zou S, Gelfand MS, Rautian MS, New Intranuclear Symbiotic Bacteria from Macronucleus of Paramecium putrinum—“Candidatus Gortzia Yakutica”, Diversity 12(5), 198.
Preprint is available at bioRxiv.
- genome_16S_merged.bed - interval file for 16S sequences identified in whole genomes;
- yakut_v6g.fa - initial compendium of 79 sequences used in the analysis;
- yakut_v6g_trim.fa - trimmed multiple sequence alignment, used in phylogeny and sequence similarity analysis;
- distances_17_spp.tsv - pairwise similarities between representative sequences;
- yakut_v6r2_trim.fa,yakut_v6r2_trim.nex - same as yakut_v6g_trim.fa, but with simplifies sequence names. Nexus file is used for MrBayes.
All scripts necessary to re-do the analysis and data visualisation from the paper are available in /scripts.
All commands are listed with comments in commands.sh. R script is used to create Figure 5.
Pairwise similarities are calculated from yakut_v6g_trim.fa using msa_to_pairwise.pl.