Licensed Software

The lab has a license for the software below. See Peter for license numbers.

Alsoft DiskWarrior
A file utility for directory maintenance.

Bookends
A reference database that provides automated formatting of references.

Crossover Pro for Mac
Run Windows programs in Mac OS X

FileMaker Pro
Database software


Geneious
Sequence alignment and feature identification.

iWork 11
Keynote, Numbers, and Pages for presentations, spreadsheets, and word processing.

MacJournal
A digital notebook, especially useful for snippets of code and other random digital bits.

Microsoft Office 2011
Excel, PowerPoint, Word, etc.

OmniGraffle
For diagrams, process charts, and organized illustrations.

Paperless 2.0
For receipt and purchase tracking

RapidWeaver
Simplified website creation

Transmit 4
FTP, secure FTP, and local mounting of remote drives from Linux/UNIX machines.

Resources

Minnesota Supercomputing Institute
This is how we do what we do! See links below for software available through MSI and for computational training through MSI tutorials.
MSI Software
MSI Tutorials

Reading the Classics

Cavalli-Sforza LL (1966) Population structure and human evolution. Proc R Soc Lond B Biol Sci 164: 362-379.

Kimura M, Crow JF (1964) The number of alleles that can be maintained in a finite population. Genetics 49: 725-738.

Charlesworth B, Morgan MT, Charlesworth D (1993) The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.

Ewens WJ (1972) The sampling theory of selectively neutral alleles. Theor Popul Biol 3: 87-112.

Felsenstein J (1974) The evolutionary advantage of recombination. Genetics 78: 737-756.

Fu Y-X, Li W-H (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.

Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society B: Biological Sciences 205: 581-598.

Hill WG, Robertson A (1966) The effect of linkage on limits to artificial selection. Genet Res 8: 269-294.


Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 111: 147–164.

Hudson RR, Kreitman M, Aguade M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.

Hudson RR (1990) Gene genealogies and the coalescent process. Oxf Surv Evol Biol 7: 1–42.

Kimura M (1968) Evolutionary rate at the molecular level. Nature 217: 624.

Kimura M (1969)
Number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics. 61: 893–903.

Kimura M, Ota T (1971) Protein polymorphism as a phase of molecular evolution. Nature 229: 467-469.

Kreitman M (1983) Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304: 412-417.

Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genet 22: 139-144.

Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.

Lewontin RC (1964) The interaction of selection and linkage. I. general considerations; heterotic models. Genetics 49: 49-67.

Lewontin RC, Hubby JL (1966) A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics 54: 595-609.

Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195.

McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.

Muller HJ (1950) Our load of mutations. Am J Hum Genet 2: 111-176.

Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273: 1516-1517.

Smith JM, Haigh J (1974) The hitchhiking effect of a favorable gene. Genet Res 23: 23-35.

Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.

Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 3: 585-595.

Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256-276.

Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.

Links - Computational Tools from Various Research Groups

DNA Sequence Assembly & Analysis
ANGSD
angsd-wrapper
bamtools
Bcftools
bedtools
bioawk
Bowtie 2
BWA
fastPHASE & PHASE
Genome Analysis Toolkit (GATK)
libsequence
Novoalign
Picard
PolyPhred
SAMTools
Scythe
seqqs
seqtk
VCFtools

Genetic Assignment
ADMIXTURE
CLUMPP
distruct
infocalc
InStruct
SCAT
Structure
Structurama
TESS

Genotyping & SNP Data
Alchemy

Marker & QTL Analyses
Eva Chan's R Scripts
heirfstat
LDheatmap
plink
R/QTL

Simulation Tools
fwdpp
macs
ms
msms
SFS_CODE

Page Updated: 21 May 2015