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IMgc Online
      
   

Go crazy!

Select an aligned fasta file:

Output File Format:
Fasta IM file body (without header)
Minimize missing data?  
Chromosome copy weight (See Notes)
Forcibly include outgroup sequence?
Find four-gamete violations in outgroup?
 


You can test IMgc with this example file.

IMgc is written in Perl. The source code and installation instructions are available for download

Please cite IMgc as:

Woerner, A.E., M.P. Cox and M.F. Hammer. (2007) Recombination-Filtered Genomic Datasets by Information Maximization. Bioinformatics23:1851-1853. PDF

Questions and comments may be directed to:

August Woerner
Murray Cox
Michael Hammer

About IMgc Online:

IMgc reads an aligned fasta file and returns the largest non-recombining block of DNA sequence. This is necessary for downstream analyses that require datasets with no evidence of recombination (such as Jody Hey's IM). IMgc maximizes the information content of the final dataset (as defined by the user). Users can favour retention of segregating sites relative to individuals, or vice versa. IMgc defaults to an equal weighting of individuals and segregating sites.

Notes

The chromosome copy weighting parameter α changes the retention of chromosome copies Cr relative to segregating sites Sr. This relationship is defined by the inclusiveness score I, such that

I = SrCrα
Indels are included for purposes of identifying four-gamete violations. Sequence data must be haplotypic and fully phased (i.e., ambiguity codes are not allowed). The characters GATCN– are permitted, where N signifies missing data and – indicates an indel.

Complex multi-base indels are sometimes observed, e.g.: ATT
--T
ATT
--T
---
 

IMgc treats these three bases as a single unit. This is an infinite sites violation, and IMgc currently changes all but the two highest frequency character states at a site violating the infinite sites model to N.

The example above would become:      ATT
--T
ATT
--T
NNN
 
 
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