BADGER

Bayesian Analysis to Describe Genomic Evolution by Rearrangement

Version 1.02 beta, June 11, 2004

Copyright © 2004 by Bret Larget & Don Simon


Input format


The program badger requires a data file which contains the genome arrangement sequences for at least two taxa. The format for the file is a series of lines, one for each taxon. Each line consists of the name of the taxon, followed by a comma, followed by a comma-separated list of genes. Gene names may be integers or any strings (not containing commas) and may be preceded by a minus sign ("-").

Here is an example of an input file:


CHOR Human,cox1,cox2,atp8,atp6,cox3,nad3,nad4L,nad4,nad5,-nad6,cob,rrnS,rrnL,nad1,nad2
CHOR Domestic Chicken,cox1,cox2,atp8,atp6,cox3,nad3,nad4L,nad4,nad5,cob,-nad6,rrnS,rrnL,nad1,nad2
HEMI Acornworm,cox1,cox2,atp8,atp6,cox3,nad3,nad4L,nad4,nad5,cob,-nad6,rrnS,rrnL,nad1,nad2
ECHI Sea star,cox1,nad4L,cox2,atp8,atp6,cox3,nad3,nad4,nad5,-nad6,cob,rrnS,-rrnL,-nad2,-nad1
ECHI Sea urchin,cox1,nad4L,cox2,atp8,atp6,cox3,nad3,nad4,nad5,-nad6,cob,rrnS,nad1,nad2,rrnL
ECHI Crinoid,cox1,nad4L,cox2,atp8,atp6,cox3,nad3,nad4,nad5,-nad6,cob,-rrnS,-rrnL,-nad2,-nad1
BRACH Laqueus rubellus,cox1,cob,atp6,nad5,nad6,nad3,nad4L,cox3,atp8,nad2,cox2,rrnL,rrnS,nad1,nad4
BRACH T. transversa,cox1,cob,atp8,cox3,atp6,nad5,rrnS,nad6,rrnL,nad1,nad4,nad4L,cox2,nad3,nad2
BRACH T. retusa,cox1,cox2,atp8,atp6,rrnS,rrnL,nad1,nad6,cob,nad4L,nad4,nad5,cox3,nad3,nad2
ANNE Common earthworm,cox1,cox2,atp8,cox3,nad6,cob,atp6,nad5,nad4L,nad4,rrnS,rrnL,nad1,nad3,nad2
ARTH Cattle tick,cox1,cox2,atp8,atp6,cox3,nad3,-nad1,-rrnL,-rrnS,-nad5,-nad4,-nad4L,nad6,cob,nad2
ARTH Fruit fly,cox1,cox2,atp8,atp6,cox3,nad3,-nad5,-nad4,-nad4L,nad6,cob,-nad1,-rrnL,-rrnS,nad2
ARTH Hermit crab,cox1,cox2,nad3,nad2,atp8,atp6,cox3,-nad5,-nad4,-nad4L,nad6,cob,-nad1,-rrnL,-rrnS
ARTH Wallaby louse,cox1,cox3,nad1,cob,-nad4,-nad4L,nad2,-nad5,cox2,-nad3,-rrnL,-rrnS,-atp6,-atp8,nad6
MOLL Squid,cox1,cox2,-nad5,-nad4,-nad4L,atp8,atp6,cox3,nad3,-cob,-nad6,-nad1,-rrnL,-rrnS,nad2
MOLL Black chiton,cox1,cox2,atp8,atp6,-nad5,-nad4,-nad4L,-cob,-nad6,-nad1,-rrnL,-rrnS,cox3,nad3,nad2
MOLL Land snail nemoralis,cox1,rrnL,nad6,nad5,nad1,nad4L,cob,cox2,-atp8,-atp6,-rrnS,-nad3,-cox3,nad4,nad2
MOLL Sea slug,cox1,rrnL,nad6,nad5,nad1,nad4L,cob,cox2,-atp8,-atp6,-rrnS,-nad3,nad4,-cox3,nad2
NEMA T. spirallis,cox1,cox2,nad1,-nad2,-nad5,-nad4,-nad4L,nad6,cob,rrnS,rrnL,atp6,cox3,atp8,nad3

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This page was most recently updated on June 29, 2004.

badger@badger.duq.edu