Vertebrate gene family trees

This is a dataset of phylogenies for 118 vertebrate gene families, used in two papers published by James Cotton and Roderic Page in 2002. The folder named "genes.zip" contains FASTA and NEXUS sequence files, and Newick-format tree files for each gene family. There is a PDF file "suppl.pdf" listing the names of each family. The file "final_dataset.gml" contains a graph of the taxonomic overlap in the gene trees. All 118 gene trees have been combined into the file "final_dataset.gtr" which is a NEXUS file with custom blocks recognised by GeneTree.

HOVERGEN FAMILY CODE
GENE FAMILY NAME

FAM000030A
wnt 5

FAM000030B
wnt 7

FAM000030C
wnt 11

FAM000030D
wnt/int 1

FAM000030E
wnt 4

FAM000030F
wnt 10/12

FAM000030G
wnt 3

FAM000030H
wnt 2

FAM000030I
wnt 8

FAM000105
rhodopsin

FAM000214
beta-B globin

FAM000033
protamine 1

FAM000370
PrP a prion-protein

FAM000014
growth hormone

FAM000556
Rag-1 recombination activation gene

FAM001493
c-mos proto-oncogene

FAM001462
tyrosine kinase / yes / fyn / src / lck

FAM001041
metallothionein

FAM000364
Ldh-2 lactate dehydrogenase-B (EC

FAM000215
alpha globin

FAM000016
placental lactogen - prolactin

FAM000008
insulin

FAM000824
phosphoglycerate kinase

FAM000550
neurotrophin-4 (NT-4)

FAM001478
tyrosine kinase receptor, c-fms oncogene

FAM000173A
guanine nucleotide-binding protein

FAM000173B
transducin alpha

FAM000502
cytochrome P-450 aromatase

FAM000192
alpha-fetoprotein / serum albumin

FAM000627
neurone-specific enolase

FAM001232
preprotrypsin (ta)

FAM000664
complement component 3 (C3)

FAM000175
Ras

FAM000248
alpha B-crystallin

FAM000006
insulin-like growth factor II

FAM000639
transthyretin (prealbumin)

FAM001303
butylcholinesterase (BCHE)

FAM000242
connexin / gap junction protein

FAM000058
dopamine D1 receptor

FAM000055
beta-3-adrenergic receptor .

FAM000131
ATPase (Na+K+, H+K+)

FAM003983
preprogastrin

FAM000353
vasopressin

FAM000152
acetylcholine receptor

FAM001327
peripherin, desmin, vimentin, GFAP

FAM003199
(C57BL/6J)

FAM002881
cytochrome P-450, 17a-hydroxylase (CYP17)

FAM002789
(MUAHRB-1) Ah-receptor (Ah)

FAM001461
tropomyosin

FAM000385
Y3 peptide supply factor

FAM000378
pancreatic polypeptide, neuropeptide Y

FAM001329
cytokeratin

FAM001619
amelogenin (enamel-specific protein)

FAM000286
glucagon

FAM000330
tissue inhibitor of

FAM000475
lipophilin

FAM001060
ornithine carbamoyltransferase

FAM001328
neurofilament

FAM001370
peroxisome proliferator

FAM000371
somatostatin

FAM001607
Wilms tumor assocated protein (WT1)

FAM000495
aldolase A, B, C

FAM001365
liver receptor homologous protein (LRH-1)

FAM000672
ribosomal protein S4,

FAM000135
Na, K-ATPase beta-1 subunit

FAM000271
enkephalin : 1 2.

FAM000799
RING10

FAM001664
glutamate decarboxylase

FAM000617
creatine kinase

FAM001337
amyloid beta protein precursor

FAM000274
basic fibroblast growth factor (bFGF)

FAM001108
Sl-d mutant allele kit ligand (KL)

FAM000504
anion exchange protein 3

FAM001239
prothrombin

FAM001360
high mobility group proteins HMG1 and HMG2

FAM000534
glutamine synthetase

FAM001053
nucleoside diphosphate kinase

FAM001390
low density lipoprotein receptor LDLR

FAM001464
Cek6 receptor tyrosine kinase

FAM000801
manganese-containing superoxide

FAM003946
Six2 / Six1 mRNA

FAM001606
Ikaros binding protein (Ikaros)

FAM000350
SPARC protein

FAM001339
calcium-binding protein

FAM000553
pyruvate kinase

FAM000604
t complex polypeptide 1 (Tcp-1-a)

FAM002988
mSlo

FAM001266
transcription factor / hepatocyte nuclear factor

FAM000453
terminal deoxynucleotidyltransferase

FAM001642
transformation associated protein p53

FAM000300A
glucose-regulated protein 78 / HSP70 PART A

FAM000300B
glucose-regulated protein 78 / HSP70 PART B

FAM000492A
alpha actin etc

FAM000492B
beta actin etc

FAM000649
Myelin Basic Protein

FAM000843
ribosomal protein S4

FAM000170
atrial natriuretic protein

FAM000871A
tyrosinase

FAM000871B
tyrosinase related protein 1

FAM001605
ZFX put. transcription activator

FAM001479
fibroblast growth factor

FAM000160
pro-opiomelanocortin (POMC)

FAM001644
fibrinogen alpha subunit

FAM000564
SNAP-25

FAM000266
nitric oxide synthase

FAM004159
chondroitin-6 sulfotransferase

FAM000800
Lmp-2 (LMPq) proteasome subunit

FAM001595
factor B

FAM001134
zona pellucida (ZP)

FAM001632
stromelysin-3

FAM001366
steroid receptor (TR2-9)

FAM000526
c-ski protein

FAM002463
thymosin beta 4 peptide

FAM000904
sequence-specific DNA-binding protein (AP-2)

FAM001465
T-cell specific tyrosine kinase (ltk)

FAM000567
triosephosphate isomerase

FAM006113
DNA-dependent RNA polymerase III, large subunit

FAM001733
DNA-dependent RNA polymerase II