Oct 23, 2018

PoSE: visualization of patterns of sequence evolution using PAML and MATLAB

BMC Bioinformatics
Kun ZhaoJaume Jorba


Determining patterns of nucleotide and amino acid substitution is the first step during sequence evolution analysis. However, it is not easy to visualize the different phylogenetic signatures imprinted in aligned nucleotide and amino acid sequences. Here we present PoSE (Pattern of Sequence Evolution), a reliable resource for unveiling the evolutionary history of sequence alignments and for graphically displaying their contents. Substitutions are displayed by category (transitions and transversions), codon position, and phenotypic effect (synonymous and nonsynonymous). Visualization is accomplished using MATLAB scripts wrapped around PAML (Phylogenetic Analysis by Maximum Likelihood), implemented in an easy-to-use graphical user interface. The application displays inferred substitutions estimated by baseml or codeml, two programs included in the PAML software package. PoSE organizes patterns of substitution in eleven plots, including estimated non-synonymous/synonymous ratios (dN/dS) along the sequence alignment. In addition, PoSE provides visualization and annotation of patterns of amino acid substitutions along groups of related sequences that can be graphically inspected in a phylogenetic tree window. PoSE is a useful tool t...Continue Reading

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Mentioned in this Paper

Computer Software
Phylogenetic Analysis
Sequence Analysis
Codon Genus
Codon (Nucleotide Sequence)
Chemical Substitution
Non-synonymous Coding SNP
Missense Mutation

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