GEOSEQ: a Pascal program to calculate statistical geometry parameters of aligned nucleic acid sequences.
Statistical geometry in sequence space is a statistical method used mainly to determine the topology of the divergence (i.e. tree, bundle or net) of a set of aligned sequences by combining horizontal and vertical positional information. GEOSEQ is a documented program written in Pascal that calculates the statistical geometry parameters necessary to choose between phylogenetic topologies. The input file is an optimal alignment of nucleic acid sequences in PHYLIP format (v. 3.3) with a first line containing information regarding sequences as well as some options. In order to check the randomization level associated with the obtained topology, the program has been implemented with a random generator of sequences under specified set conditions.
López-Bueno
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Departamento de Genética, Facultad de Biología, Valencia, Spain.
Moya
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D000465:Algorithms; D001483:Base Sequence / Q000235:genetics*; D008432:Mathematical Computing; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D012984:Software