#co-phylog tools set

Please cite: “Co-phylog: an assembly-free phylogenomic approach for closely related organisms H Yi, L Jin Nucleic acids research 41 (7), e75-e75”

======INSTALL AND USAGE========

1. Compile:

gcc fasta2co_v18.3.c -O6 -Wall -o fasta2co ;

gcc fastq2co.c -O6 -Wall -o fastq2co ;

gcc co2dist2.c -O6 -Wall -o co2dist ;

gcc readco.c -Wall -o readco ;

2. Usage:

fasta2co : Convert fasta file to co file ; Usage : ./fasta2co <.fasta> <.co>

fastq2co: Convert fastq file to co file ; Usage : ./fasta2co <.fastq> <.co>

readco: read binary co file Usage : ./readco <string/hex>

co2dist: generated pairwise distance from co files Usage: ./co2dist > *.dist

dis_matr_ge.pl: Generated standard distance matrix and orangnism name code from pairwise distances Usage : perl ./Pl/dis_matr_ge.pl [pairwise distances file] [organism number] >[output file]

nwkrename.pl When using 'neighbor' in Phylip package to generated tree file. if you need substitute the output code using origin organism name,you could use this program Usage: perl ./Pl/nwkrename.pl [outtree/outfile] > [output file]

EXAMPLE:

tar xzvf example_brucella.tar.gz
cp example_brucella/* algorithm/Genomes/
cd algorithm

1) Build cofile files using complete genomes

	for i in `ls Genomes`;
		do ./C/fasta2co ./Genomes/$i ./CO-index/$i.co ;
	done;

You can also bulid co file using fastq NGS data by:
   for i in `ls Genomes`;
       do ./C/fasta2co ./Genomes/$i ./CO-index/$i.co ;
	done;

2) Generate pairwise distances using index files
./C/co2dist CO-index >dist

3) format the pairwise distances to standard distance matrix
        perl ./Pl/dis_matr_ge.pl dist 15 >dis_matrix

4) If the 'neighbor' contained in Phylip package has been installed then
		neighbor <<END
					dis_matrix
					Y
		        END

5) If want to replace the namecode by organisms' name								    
	perl ./Pl/nwkrename.pl outtree