PoSE: visualization of patterns of sequence evolution using PAML and MATLAB
Abstract Background 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. Results Here we present PoSE (...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-10-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-018-2335-7 |
| _version_ | 1811336934145916928 |
|---|---|
| author | Kun Zhao Elizabeth Henderson Kelley Bullard M. Steven Oberste Cara C. Burns Jaume Jorba |
| author_facet | Kun Zhao Elizabeth Henderson Kelley Bullard M. Steven Oberste Cara C. Burns Jaume Jorba |
| author_sort | Kun Zhao |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. Conclusions PoSE is a useful tool to help determine major patterns during sequence evolution of protein-coding sequences, hypervariable regions, or changes in dN/dS ratios. PoSE is publicly available at https://github.com/CDCgov/PoSE |
| first_indexed | 2024-04-13T17:47:38Z |
| format | Article |
| id | doaj.art-2d4ef86a8d6e432787d9d8b2b37c5a86 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T17:47:38Z |
| publishDate | 2018-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-2d4ef86a8d6e432787d9d8b2b37c5a862022-12-22T02:36:53ZengBMCBMC Bioinformatics1471-21052018-10-0119S111710.1186/s12859-018-2335-7PoSE: visualization of patterns of sequence evolution using PAML and MATLABKun Zhao0Elizabeth Henderson1Kelley Bullard2M. Steven Oberste3Cara C. Burns4Jaume Jorba5Polio and Picornavirus Laboratory Branch, G-10, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and PreventionPolio and Picornavirus Laboratory Branch, G-10, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and PreventionIHRC Inc.Polio and Picornavirus Laboratory Branch, G-10, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and PreventionPolio and Picornavirus Laboratory Branch, G-10, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and PreventionPolio and Picornavirus Laboratory Branch, G-10, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and PreventionAbstract Background 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. Results 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. Conclusions PoSE is a useful tool to help determine major patterns during sequence evolution of protein-coding sequences, hypervariable regions, or changes in dN/dS ratios. PoSE is publicly available at https://github.com/CDCgov/PoSEhttp://link.springer.com/article/10.1186/s12859-018-2335-7Molecular evolutionBioinformaticsPhylogeneticsMATLABPAML |
| spellingShingle | Kun Zhao Elizabeth Henderson Kelley Bullard M. Steven Oberste Cara C. Burns Jaume Jorba PoSE: visualization of patterns of sequence evolution using PAML and MATLAB BMC Bioinformatics Molecular evolution Bioinformatics Phylogenetics MATLAB PAML |
| title | PoSE: visualization of patterns of sequence evolution using PAML and MATLAB |
| title_full | PoSE: visualization of patterns of sequence evolution using PAML and MATLAB |
| title_fullStr | PoSE: visualization of patterns of sequence evolution using PAML and MATLAB |
| title_full_unstemmed | PoSE: visualization of patterns of sequence evolution using PAML and MATLAB |
| title_short | PoSE: visualization of patterns of sequence evolution using PAML and MATLAB |
| title_sort | pose visualization of patterns of sequence evolution using paml and matlab |
| topic | Molecular evolution Bioinformatics Phylogenetics MATLAB PAML |
| url | http://link.springer.com/article/10.1186/s12859-018-2335-7 |
| work_keys_str_mv | AT kunzhao posevisualizationofpatternsofsequenceevolutionusingpamlandmatlab AT elizabethhenderson posevisualizationofpatternsofsequenceevolutionusingpamlandmatlab AT kelleybullard posevisualizationofpatternsofsequenceevolutionusingpamlandmatlab AT mstevenoberste posevisualizationofpatternsofsequenceevolutionusingpamlandmatlab AT caracburns posevisualizationofpatternsofsequenceevolutionusingpamlandmatlab AT jaumejorba posevisualizationofpatternsofsequenceevolutionusingpamlandmatlab |