To run the complete pipeline, In the WGA folder run:
./run_all.pl [ref_genome.fasta] [query1_genome.fasta] ... [query#_genome.fasta]

This program goes through following steps:
Steps followed: 
-- run mummer : 
-- -- promummer reference.fasta query.fasta 
-- -- show_coords -bTH out.delta > new.coords
This runs mummer with minimum match length of 20
-- Fetch Gaps
-- -- perl get_promum.pl new.coords > coords_by_org
-- -- perl get_gaps.pl coords_by_org > gaps.fasta
-- -- perl show-gaps2.pl gaps.fasta [ref_genome.fasta] [query1_genome.fasta] ... [query#_genome.fasta]
Show-gaps2 will generate xNumber of genome_gaps.fasta
-- Create Blast Database
-- -- perl blast_all.pl [ref_genome_gaps.fasta] [query1_genome_gaps.fasta] ... [query#_genome_gaps.fasta]
-- Build orthlogs
-- -- perl get-ortholog-pair.pl ref_query.out1 ref_query.out2 > ortholog_list
Getting ortholog pairs script has to be run on all reciprocal blast searches to compile all orthologs
-- -- perl get_ortholog_seq.pl ortholog_list > multi_gap_alignment.txt


Viewing the alignment requires the following steps:
-- Viewing Multi-Genome Gap Alignment
-- -- Access Online Viewer at: http://cas-bioinfo.cas.unt.edu/mgsv/index.php
-- -- Choose File : multi_gap_alignment.txt
-- View the original MUMmer alignment in the same manner
-- -- perl mummer2mgsv.pl new.coords > Original_alignment.txt
-- -- Access Online Viewer at: http://cas-bioinfo.cas.unt.edu/mgsv/index.php
-- -- Choose File : Original_alignment.txt