EvolGenius
This is a 2-locus population genetics simulation intended mainly for classroom use.
Microscan_rk2 (perl)
This a modification of Mohamed Noor's perl program to search a Fasta library for microsatellites. The user chooses the size of the repeat (mono-, di, tri-, tetranucleotide, etc.), the minimum number of repeats, and the minimum number of bases of flanking sequence. Remove the .txt suffix after downloading.
LU1
This program reads GenBank files and produces an output file with the following information for each CDS: the name of the GenBank file, the gene name, the CDS (in GenBank format), and the contig.
LU2
This program reads the output file produced by LU1. It produces an output file with the following information for each gene: the name of the GenBank file, the gene name, the first CDS listed for that gene (if more than one), the number of listings for the gene, the number of alternative CDSs for the gene, and the contig.
CODON10
This program reads the output file produced by LU2 (henceforth referred to as the "lookup table"). CODON10 has two modes, "check" and "analysis". In "check" mode, CODON10 examines the lookup table for problems that indicate incorrect annotation (e.g., a CDS length that is not a multiple of 3) or incomplete annotation (e.g., an incomplete CDS). In "check" mode, CODON10 also looks for consecutively listed genes with overlapping CDSs. [It should be noted that in "analysis" mode, CODON10 can not handle CDS overlaps involving more than two genes.]
In "analysis" mode, CODON10 uses the information in the lookup table
to read the GenBank file(s) and analyze the genes (in order of
appearance in the lookup table) with
respect to codon usage and base composition. It will read up
to 1000 bases of flanking sequence on either side of the start and
stop codons, as long as the flanking sequence does not overlap an
adjacent CDS.
Please do not hesitate to send me suggestions, or to ask questions,
by email (rmkliman@cedarcrest.edu). Our research requires continually updated
versions of LU1, LU2 and CODON10. These are available upon
request. Also, software associated with Llopart et al. (2008, MONTECOD) and McDermott &
Kliman (2008, ISOLATION) is available upon request.
The most appropriate citation for EvolGenius is
Kliman, R.M. (2002) A project-based approach to teaching
complex population genetics to undergraduates. Bioscence: The Journal
of College Science Teaching 27(4): 13-20. The most appropriate citation
for LU1, LU2 or CODON10 is
Kliman, R.M., N. Irving and M. Santiago (2003) Selection
conflicts, gene expression and codon usage trends in yeast. Journal of Molecular
Evolution 57: 98-109.