Arthropod Phylogenomics:
Software and Useful Scripts
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Note: This page is in Progress.

One key piece of software to appear here shortly will be a C++ program to allow users to implement a variety of recoding schemes on aligned nucleotide sequence data.

Software: ReCoDer 1.1

I have several simply coded custom scripts to interact with the program. Each allows a different method of sequence data recoding, e.g. selecting all 3rd codon positions to be replaced with an R (purine) for A or G bases or Y (pyrimidine) for C or T bases. This recoding scheme is quite widely used for deep-level phylogenetics, called something like RY coding.

See: http://mbe.oxfordjournals.org/cgi/content/full/21/7/1455

Matthew J. Phillips, Frédéric Delsuc and David Penny (2004). Genome-Scale Phylogeny and the Detection of Systematic Biases. Mol. Biol. Evol. 21(7):1455-1458.

Further to RY coding, this software allows certain codons to be treated with exception, e.g. for select codons like ATG to remain asis, rather than recoding every of 3rd position throughout the dataset [so ATG does not get changed to ATR]. Coversely, certain codons can be selected for specific replacement, e.g. only AGG codons are recoded as completely ambiguous [to NNN], or only third positions in AGG codons treated as ambiguous [to AGN], or just to replace 3rd positions of AGG codons with RYcoding, to AGR. A myriad of recoding options.

If you think you are interested in using this program, please email me (stul-at-pdx.edu), and i can provide a copy and support. It is only available for Mac OSX users currently.

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Below is something a computer scientist once wrote to me. It took me several years before i understood what he meant.

"There are 10 types of people, those that understand binary code, and those that don't."

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*** *** Drosophila yakubaCAAGATAGAGCTTCTCCTTTAATGGAACAATTAATT