Data Files for Geobiology (2003) Genomic Publication

House, C.H., Runnegar, B., Fitz-Gibbon, S.T. 2003. Geobiological analysis using whole genome-based tree building applied to the Bacteria, Archaea, and Eukarya. Geobiology, 1: 15-26.


Data Matrix Files:
neb9_160i.nex  (no eukaryotes/big.  55 taxa.  Figure 1a, b & c):
aa,af,ap,at,bh,bm,bs,ca,cc,cg,cj,cpe,cte,dr,ec,fn,hi,hp,hsp,ll,ma,mj,mk,ml,mle,mma,mt, mtb,nmm,nmz,ns,pa,pab,pf,ph,pm,psa,rs,sam,sco,sm,sp,ss,st,sty,sy,ta,tm,tt,tv,vc,xa,xc,
xf,yp

euks_160i.nex (eukaryotes, plus archaeal outgroup.  8 taxa.  Figure 4):
ap,ath,ce,dm,hsa,pag,sc,ss


Prokaryotes:
ap        Aeropyrum pernix
at         Agrobacterium tumefaciens
aa         Aquifex aeolicus
at         Archaeoglobus fulgidus
bh        Bacillus halodurans
bs        Bacillus subtilis
bm       Brucella melitensis
cj         Campylobacter jejuni
cc         Caulobacter crescentus (vibroides)
cte        Chlorobium tepidum
ca         Clostridium acetobutylicum
cpe       Clostridium perfringens
cg        Corynebacterium glutamicum
dr         Deinococcus radiodurans
ec         Escherichia coli
fn         Fusobacterium nucleatum
hi         Haemophilus influenzae Rd
hsp      Halobacterium sp.
hp        Helicobacter pylori
ll          Lactococcus lactis
ml        Mesorhizobium loti
mt        Methanobacterium thermoautotrophicum
mj        Methanococcus jannaschii
mk       Methanopyrus kandleri
ma       Methanosarcina acetivorans
mma    Methanosarcina mazei
mle      Mycobacterium leprae
mtb      Mycobacterium tuberculosis
nmm    Neisseria meningitidis
nmz     Neisseria meningitidis
ns        Nostoc sp.
pm       Pasteurella multocida
psa       Pseudomonas aeruginosa
pa        Pyrobaculum aerophilum
pab      Pyrococcus abyssi
pag      Pyrobaculum aerophilum
pf         Pyrococcus furiosus
ph        Pyrococcus horikoshii
rs         Ralstonia solanacearum
sty       Salmonella typhimurium
sm       Sinorhizobium meliloti
sam      Staphylococcus aureus
sp        Streptococcus pyogenes
sco       Streptomyces coelicolor
ss         Sulfolobus solfataricus
st         Sulfolobus tokodaii
sy        Synechocystis sp.
tt          Thermoanaerobacter tengcongensis
ta         Thermoplasma acidophilum
tv         Thermoplasma volcanium
tm        Thermotoga maritima
vc         Vibrio cholerae
xa        Xanthomonas axonopodis pv citri
xc        Xanthomonas campestris
xf         Xylella fastidiosa
yp        Yersinia pestis

Eukaryotes:
ath       Arabidopsis thaliana
ce         Caenorhabditis elegans
dm       Drosophila melanogaster
hsa       Homo sapien
sc         Saccharomyces cerevisiae

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