/Sulfito-BSC

Primary LanguageRMIT LicenseMIT

Sulfitobacter speciation

Source code to replicate results for the manuscript "A Novel Bacterial Speciation Process Found in a Marine Symbiotic Population".

In the 01-phylogeny-construction directory:

  • Input:.pep and .gene files, the former contains amino acid sequences for each genome, and the latter contains nucleotide sequences for each genome;
  • S1.orthoFinder_blast.sh and S2.extract_scp_seq.pl prepare the single copy core orthologs sequences in both amino acids (.faa) and nucleotides (.dna);
  • Phylogenies based on 16S rRNA genes or concatenated single copy orthologs alignments can be constructed using scripts 16S_tree_constr.sh and S3*-S4*;
  • Phylogenies of each single copy orthologs can be constructed using the scripts in aa_seq and nuc_seq;
  • topo_check_outgroup_rooted.R is used to determined the topology supported by each gene tree in ./with_outgroup(gene trees each was constructed using 28 members of three clades and two outgroups based on either amino acids or nucleotides).
  • Gene trees in ./without_outgroup each was constructed using only 28 members of three clades, and rooted by MAD and MV methods, respectively. The supporting topology of each MAD-rooted gene tree was determined using topo_check_MADroot.R, and MV-rooted gene tree was determined with topo_check_MVroot.R.

In the 02-RMS-identification directory:

  • Scripts s1*-s3* identify the best hit restriction or modification enzymes for query genes;
  • The reference (R-M system) data is downloaded form REBASE;
  • The .pep containing amino acid sequences for each genome is used as the query.

Note that the R-M system for each genome should be manually check whether the genes are neighbors after getting the best hits.