/Phylogenetic-Tree-Building

A tool kit for extracting 16S rRNA genes from genomes for the purpose of building phylogenetic trees.

Primary LanguagePythonMIT LicenseMIT

Phylogenetic-Tree-Building

A tool kit for extracting 16S rRNA genes from genomes for the purpose of building phylogenetic trees.

Here is a short description of each script:

  • 16SBLAST.py - Uses NCBI's BLASTn to search for 16S genes within a query genome by querying a BLAST database which contains a variety of 16S genes.
  • 16SHMMER.py - Uses HMMER and a 16S hmm to search for 16S genes in a target genome. The script searches both the forward and reverse strand of the genome for the best 16S gene.
  • runPrimerSearch16S.sh - A shell script that uses the command-line tool grep to search for 16S primer binding sites within a genome.
  • runHMMSearchGyrase.sh - A shell script that uses HMMER to search for Gyrase B. genes within a genome.

For more thorough descriptions and information on usage please check the [wiki!] (https://github.com/LeeBergstrand/Phylogenetic-Tree-Building/wiki)