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src
MultiMSOAR2.0
README.md
S0_S1
S0_S2
S0_S3
S0_S4
S1_S2
S1_S3
S1_S4
S2_S3
S2_S4
S3_S4
sampleGeneFamily
sampleGeneFamily2
sampleSpeciesTree

README.md

MultiMSOAR 2.0: An Accurate Tool to Identify

Ortholog Groups among Multiple Genomes


Usage

The software MultiMSOAR 2.0 is an executable file included in the current directory. It requires the following files as input:

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

Run MultiMSOAR2.0

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.

Output:

	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

File Format

Si_Sj (0<=i<j<n)

  Si_gene			Sj_gene		SimilarityScore

Ex: S0_gene1 S1_gene2 105

speciesTree

	We use the Newick format to represent a species tree

Ex: ((S0,S1),(S2,(S3,S4)));

geneFamily

	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

GeneInfo

	Report the new born gene and duplicated genes in 
current genomes, and the number of lost genes in
every genome in the species tree

OrthoGroup

Each line reports genes within the same ortholog
group

Sample Input

	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