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The following are links to program source code and information on some programs that we have written and/or found useful:

Codon Usage Utitlities — programs for analyzing and comparing codon usages.

CRITICA — a program for identifying the coding sequences within DNA.

DNArates — a program for estimating site-specific rates of nucleotide change from a nucleotide sequence alignment and a phylogenetic tree.

fastDNAml — a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences.

Genetic codes — a WWW page with the NCBI genetic code tables.

Newick's 8:45 Tree Standard — my interpretation of the Newick's 8:45 Standard for representing phylogenetic trees. (text version of same document)

Newick Tree Programs and Library — some perl untility programs and a (required) subroutine library for manipulating Newick trees.

PAUP_aides — a directory of programs, procedures and files that are useful in conjunction with David Swofford's PAUP and PAUP* programs

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Page written and maintained by Gary J. Olsen (