ANC-GENE Inference of Ancestral Gene Sequences by the Distance-Based Bayesian Method
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ANC-GENE Tags

sequence Bayesian inference engine gene Fuzzy inference system nucleotide sequence inference problem variational inference Bayesian network editor edit Bayesian network inference bayesian alignment haplotype inference Inference Tool Bayesian analisis Bayesian method implementation Bayesian method Bayesian analysis distance-based analysis phylogeny inference ancestral gene cluster ancestral gene large phylogeny inference Bayesian MCMC analysis Gene Sequence statistical inference ancestral

ANC-GENE Description

The ANC-GENE application was developed to be a small command line tool for inference of ancestral nucleotide sequences of protein coding genes from a set of present-day sequences whose phylogenetic relationships are known. The program first infers the amino acids by the distance-based Bayesian method, and then infers the underlying nucleotide sequences by fixing the inferred amino acids. To use the program, you need a input file containing the DNA sequences and the tree topology of these sequences (see rnase.seq for an example). This file begins with two numbers: the number of sequences and the number of nucleotides per sequence (sequence length). The second line will be the name of the first sequence, and the third line will be the first sequence, and so on. Only A, T, C, G, a, t, c, and g are allowed in the sequences. The sequences should be aligned and gaps or any other symbols be removed. The last line of the file is the tree topology of the sequences. The tree format is the same as that used in PHYLIP package (Felsenstein 1995). Note that the tree is unrooted, so trification rather than bification is required for the deepest branching node.

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