Data files for 2014 SISG module 12

Here are the files that can be copied from this folder. One way to do it is to click on the file name. The mark all the text that appears and save it using the Save As feature of your browser's File menu. Or you can hold down the Ctrl key while selecting the file name. On some browsers this opens a menu that includes the ability to "Download linked file".

1. Some aligned DNA and protein assembled by Joe Felsenstein for teaching purposes. The primates.dna and cytb.prt are the ones used in the lecture projections.

cytb.prtCytochrome B amino acide sequences in vertebrates
mammalspenny.prtcatenation of protein sequences of mammals by D. Penny
eftualpha.prtEFTU-Alpha protein sequences in eukaryotes
primates.dnaMasami Hasegawa's collection of mitochondria control-region and nearby 3rd position DNA sequences in 14 species of primates
turbeville.dnaClint Turbeville's alignment of large-subunit RNA in vertebrates and other deuterostomes

2. Aligned DNA or protein sequences from the OrthoMAM database for a set of (in most cases) 40 mammalian species, each with its HUGO gene identifier which is used for the file name. These sequences are in Sequential format, so make sure you make that menu selection (I) when using them in PHYLIP programs. The 40-species data sets all have the same set of species, so that comparison of the trees they get is potentially of interest. Filenames ending in ".dna" are DNA sequences, those ending in ".prt" are amino acid sequences.

Here are the names of those organisms and their identities.

FilenameProtein
---------------
ADAM7.dnamember of the ADAM (A Disintegrin and Metalloprotease) gene family
AP3M2.dnaadaptor-related protein complex 3, mu 2 subunit
ASH2L.dnaset1/ash2 histone methyltransferase
CA8.dnacarbonic anhydrase VIII
CHMP4C.dnacharged multivesicular body protein 4C
DEPTOR.dnaDEP domain containing MTOR-interacting protein
DERL1.dnaDerlin 1
E2F5.dnaE2F transcription factor 5, p130-binding
ERLIN2.dnaER lipid raft associated 2
FZD6.dnafrizzled class receptor 6
GGH.dnagamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase)
GINS4.dnaGINS complex subunit 4 (Sld5 homolog)
GRHL2.dnagrainyhead-like 2
GTF2E2.dnageneral transcription factor IIE, polypeptide 2, beta 34kDa
KAT6A.dnaK(lysine) acetyltransferase 6A
LACTB2.dnalactamase, beta 2
LRP12.dnalow density lipoprotein receptor-related protein 12
LRRC6.dnaleucine rich repeat containing 6
MCMDC2.dnaminichromosome maintenance domain containing 2
mdh1.prtMalate dehydrogenase 1
MMP16.dnamatrix metallopeptidase 16 (membrane-inserted)
MTERFD1.dnaMTERF domain containing 1
NSMAF.dnaneutral sphingomyelinase (N-SMase) activation associated factor
OPRK1.dnaopioid receptor, kappa 1
RAD54B.dnaRAD54 homolog B
RRM2B.dnaribonucleotide reductase M2 B (TP53 inducible)
SART3.dnasquamous cell carcinoma antigen recognized by T cells 3
SART3.prtsquamous cell carcinoma antigen recognized by T cells 3
SLC18A1.dnasolute carrier family 18 (vesicular monoamine transporter), member 1
SNX16.dnasorting nexin 16
STC1.dnastanniocalcin 1
TMEM55A.dnatransmembrane protein 55A
TNKS.dnatankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase
TP53INP1.dnatumor protein p53 inducible nuclear protein 1
VCPIP1.dnavalosin containing protein (p97)/p47 complex interacting protein 1
WRN.dnaWerner syndrome, RecQ helicase-like
WWP1.dnaWW domain containing E3 ubiquitin protein ligase 1