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  1. Phrecon (PHylo RECONstructor) -- This script reconstructs the base sequence using an SNP loci and substituting its bases in at the given locations in the provided reference base sequence.

    Python 1

  2. Prephix (Pre-Phrecon Input fiXer) -- This is a script that takes in a list of input files and generates one SNP loci output file (containing multiple strains), one reference base file, and a file c…

    Python 1 1

  3. Script for extracting Coding DNA Sequence (CDS) values from a GB file.

    Perl 2

  4. A script that matches and returns an ST type number for a given base reference sequence, MLST fragment files (all fasta formatted), and ST type table file.

    Perl

  5. This script reconstructs the base sequence using a base reference sequence in FASTA format, and a SNP loci file and indel file produced by prephix. It then does substituting, inserting, or deleting…

    Perl

  6. Parses BLAST result files and tabulates the top hits for each query and prints out a report.

    Python

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