1001 - A tool for binary representations of unordered multistate characters (with examples from genomic data)

Abstract. In modern molecular systematics, matrices of unordered multistate characters, such as DNA sequence alignments, are used for analysis with no further re-coding procedures nor any a priori determination of character polarity. Here we present 1001, a simple freely available Python-based tool that helps re-code matrices of non-additive characters as different types of binary matrices. Despite to the historical basis, our analytical approach to DNA and protein data has never been properly investigated since the beginning of the molecular age. The polarized matrices produced by 1001 can be used as the proper inputs for Cladistic analysis, as well as used as inputs for future three-taxon permutations. The 1001 binary representations of molecular data (not necessary polarized) may also be used as inputs for different parametric software. This may help to reduce the complicated sets of assumptions that normally precede either Bayesian or Maximum Likelihood analyses.