Programs

Computer Programs
for DNA & population genetic analysis
used in the SREL DNA Lab

Programs developed at SREL &/or USC:

Mac -

Ephemeris 1.0 - is used to automatically screen sequences for microsatellite repeats. This is especially useful when you have an ABI gel full of microsatellite clone sequences.   Ephemeris 1.0 ReadMe describes this PERL program in detail.

Bottleneck SimulatER 1.0-beta - is used to determine the effects of small population size on allele frequencies (Glenn et al. 1999, Cons. Biol. 13:1097-1107).  Bottleneck SimulatER 1.0 ReadMe

Programs developed elsewhere:

Mac -

Arlequin 2001 - is used to test population structure via Analysis of Molecular Variance (AMOVA) and to calculate many measures of nucleotide diversity, selection, etc. (a PC version is also available).

BBedit Lite 6.1 - is used to put sequence alignments together in text files for specific analysis programs (e.g., PAUP). Some helpful template files are: ArlequinHeader.txt [link]; GenePopHeader.txt; & PaupHead.txt.

PAUP*4.0 - is used to construct phylogenetic trees. Also available in inferior (command line) versions for other OS's.

Sequencher 4.1.2 - is used to edit our ABI sequence files & generate simple restriction maps. A PC version is also available.

TreeView 1.5.3 - is used to quickly print reasonably nice phylogenetic trees. Also available for other OS's.

PC -

Arlequin 2001 - is used to test population structure via Analysis of Molecular Variance (AMOVA) and to calculate many measures of nucleotide diversity, selection, etc. (a Mac version is also available).

GenePop 3.1 - is used to estimate most standard population genetic parameters (e.g., Hardy-Weinberg Tests; Population Differentiation; Fst & Rho-st).

Sequencher 4.0 - is used to edit our ABI sequence files & generate simple restriction maps. A Mac version is also available.

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