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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.

The base reference should only have TWO columns (and no headers), consisting of just the base location and base.

The SNP input file may contain multiple SNP "fragments" (ids), and phrecon will generate a new sequence for each one
and write them out in FASTA format into the same output file.

SNP file input should contain three columns and no headers:
SNP_ID (i.e. query id) | Base position | Base

So something like:
A12 1045  G
A12 4056  A
A12 13004 T
A35 4 A
A35 401 C

The above example contains two query SNPs, so phrecon will generate a FASTA file containing the full sequence for each.

Prephix's SNP and base ref output files can be used by phrecon as input.

Usage: phrecon.pl <reference base file> <SNP loci input file>