Example

Example 1 (A simple illustration).

Consider the small case of this haplocount file,
 Download the txt file http://sourceforge.net/projects/virhap/files/haplocount.txt or symply create a csv
file with the following contain and name it haplocunt.csv:

set 1
Clones,M1,M2,Counts
C00,0,0,1562
C01,0,1,921
C10,1,0,17
C11,1,1,3220
set 2
Clones,M2,M3,Counts
C00,0,0,562
C01,0,1,1021
C10,1,0,2230
C11,1,1,23

 run the following command

./treeconstruct haplocount.csv

 the output obtained are :

– the following evolutionary tree in the newick format in the generated file haplocount supertree.newick:
(((0.520575-M1:0.520575,0.14891-Haplo 1:0.14891)0.669485-M2:0.14891,0.213188-M3:0.213188,0.117327-
Haplo 2:0.117327)1-Root:0.117327)SuperTree01
A visualisation using the tool FigTree ( a graphical viewer of phylogenetic trees, see http://tree.bio.ed.ac.uk/software/figtreeadding the label as branch label gives the following figure :

Example 2 (Simulated data). 

Consider and download the following files at https://sourceforge.net/projects/virhap/files/:

– ’metasim H15clonals.fasta’ containing genomes of 15 haplotypes of a simulated viral population
along with their prevalence.
– ’metasim H15.fna’ containing 10,000 simulated reads of the previous viral population using the
metagenomic simulator Metasim and replicating the Roche 454 error process.
– ’refHXB2.fa’ the reference genome file
– ’metasim H15.sam’ the sam files containing the aligned reads mapped with bowtie2
 Align the reads file ’metasim H15.fna’ to the reference using any aligner or simply use the file metasim H15.sam

 Run the shell pipeline by invoquing the following command. Note that those files are also available in
the folder Examples/Simulation/ of the idstribution.

./virhap.sh Examples/Simulation/refHXB2.fa Examples/Simulation/metasim H15 1.0 0.02

 the output gives:

– 102 evolutionary trees (see file Examples/Simulation/metasim H15 supertrees.newick). The figure
above shows one of them visualised in FigTree :
– 35 distinct haplotypes (see file Examples/Simulation/metasim H15 hapdistincts.csv). The following
figures shows a preview of the list of haplotypes