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OVERVIEW

PAULOWNIA is a python wrapper around BLAST, the alignment program MAFFT and the the fast neighbor-joining method implemented in clearcut. The purpose of the script is to efficiently add a new genome to an existing alignment, based on a set of query sequences.

USAGE

python paulownia.py <new_genome / directory_of_genomes> <query_fasta_sequences>

This assumes a single file for the new_genome, or a directory containing only fasta formatted genomes in directory_of_genomes. The query_fasta_sequences are a list of query sequences / genes for which a phylogeny should be built.

Given the query fasta sequences, paulownia generates a new concatenated alignment for each genome, based on the order of the sequences in the query_fasta_sequences file.

If an existing alignment file is specified, the new genome(s) will be added to it; if no existing alignment file is specified, a new alignment is created. In both cases a new tree is generated.

OPTIONAL ARGUMENTS and their [DEFAULTS]

  • -h,--help Displays usage information
  • -c,--clearcut_exe The location of the clearcut executable [/usr/bin/clearcut]
  • -b,--blast_dir The directory of the blast+ program suite [/usr/bin/]
  • -a,--alignment_file The previous alignment to which the new genomes(s) should be added. [previous.aln]
  • -o,--out_tree The location where the newly generated tree should be output. [new_paulownia.tre]
  • -m,--mafft_exe The location of the MAFFT executable [/usr/bin/mafft]
  • -t,--tmp_dir The location of created temporary files [/tmp/]
  • -p,--percent_id_cutoff The percent identity that a query sequence must exist at in a genome for it to be considered present and used in the alignment [90]
  • -n,--number_of_threads The number of threads to use in the creation of the new tree [1]

EXAMPLE with Salmonella enterica

584 Salmonella enterica genomes were used for analyses. Initially 330 core genes were identified, however, they were not universally present in all 584 genomes.

for i in *.aln; do if [ $(grep -c '>' $i) = 584 ]; then cp $i ~/workspace/core_tree/universal/; fi done

286 genes were determined to be universally present, which were used for subsequent tree building paulownia/data/query.fasta. The alignment of these genes for the 584 genomes is found in paulownia/data/universal_combined.aln.

To add both of the test genomes in paulownia/data/salmonella_fasta_files/:

python paulownia.py data/salmonella_fasta_files/ data/query.fasta -a data/universal_combined.aln