The software MultiMSOAR 2.0 is an executable file included in the current directory. It requires the following files as input:
speciesTree - binary species tree in Newick format
geneFamily - gene families for all input genomes
Si_Sj - ortholog pairs and their similarity
scores between genomes Si and Sj
Move all files Si_Sj to the same directory as the
the executable file MultiMSOAR2.0, then execute the
following command:
./MultiMSOAR2.0 <#species> <speciesTree> <geneFamily>
<-o GeneInfo> <-o OrthoGroup>
The <#species> is an integer, representing the number
of species in comparison. Suppose there are n species,
then we need n*(n-1)/2 files (Si_Sj, 0<=i<j<n), which
contains the orthology information between any pair of
the n genomes.
GeneInfo - the file contains information about
gene births, losses and duplications
for every input genomes
OrthoGroup - the file contains all ortholog groups
identified by MultiMSOAR 2.0
Si_gene Sj_gene SimilarityScore
Ex: S0_gene1 S1_gene2 105
We use the Newick format to represent a species tree
Ex: ((S0,S1),(S2,(S3,S4)));
Each line contains the gene names from all species
within a gene family, separated by '\t'
Ex: S0_gene1 S1_gene1 S2_gene1 S1_gene2 S2_gene2
Report the new born gene and duplicated genes in
current genomes, and the number of lost genes in
every genome in the species tree
Each line reports genes within the same ortholog
group
This directory also contains sample input files:
Si_Sj(0<=i<j<5)
sampleSpeciesTree
sampleGeneFamily
With these sample files, you can run MultiMSOAR2.0
as follows:
./MultiMSOAR2.0 5 sampleSpeciesTree sampleGeneFamily
sampleGeneInfo sampleOrthoGroup
You will get the results saved in the files
sampleGeneInfo and sampleOrthoGroup