EZmito: a simple and fast tool for multiple mitogenome analyses
Complete mitochondrial genome data are frequently applied to address phylogenetic/phylogeographic issues at different taxonomic levels in ecology and evolution. While sample preparation/sequencing is becoming more and more straightforward thanks to dropping costs for next-generation sequencing (NGS)...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2021-03-01
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| Series: | Mitochondrial DNA. Part B. Resources |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/23802359.2021.1899865 |
| _version_ | 1827772496348184576 |
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| author | Claudio Cucini Chiara Leo Nicola Iannotti Sara Boschi Claudia Brunetti Joan Pons Pietro Paolo Fanciulli Francesco Frati Antonio Carapelli Francesco Nardi |
| author_facet | Claudio Cucini Chiara Leo Nicola Iannotti Sara Boschi Claudia Brunetti Joan Pons Pietro Paolo Fanciulli Francesco Frati Antonio Carapelli Francesco Nardi |
| author_sort | Claudio Cucini |
| collection | DOAJ |
| description | Complete mitochondrial genome data are frequently applied to address phylogenetic/phylogeographic issues at different taxonomic levels in ecology and evolution. While sample preparation/sequencing is becoming more and more straightforward thanks to dropping costs for next-generation sequencing (NGS), data preparation and visualization remains a manually intensive step that may lead to errors if improperly conducted. We have elaborated, and here introduce, EZmito, a simple and intuitive, freely accessible Web Server aimed at automating some of these tasks. EZmito is divided into three main tools: EZpipe that assembles DNA matrices for phylo-mitogenomic analyses; EZskew that calculates genome, strand, and codon nucleotide compositional skews and EZcodon which computes Relative Synonymous Codon Usage statistics as well as amino acid usage frequency over multiple mitogenomes. Output is produced in tabular format as well as publication-quality graphics. |
| first_indexed | 2024-03-11T13:10:19Z |
| format | Article |
| id | doaj.art-1f6bcfe9d33045298d8a82f65efe4383 |
| institution | Directory Open Access Journal |
| issn | 2380-2359 |
| language | English |
| last_indexed | 2024-03-11T13:10:19Z |
| publishDate | 2021-03-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Mitochondrial DNA. Part B. Resources |
| spelling | doaj.art-1f6bcfe9d33045298d8a82f65efe43832023-11-03T14:16:07ZengTaylor & Francis GroupMitochondrial DNA. Part B. Resources2380-23592021-03-01631101110910.1080/23802359.2021.18998651899865EZmito: a simple and fast tool for multiple mitogenome analysesClaudio Cucini0Chiara Leo1Nicola Iannotti2Sara Boschi3Claudia Brunetti4Joan Pons5Pietro Paolo Fanciulli6Francesco Frati7Antonio Carapelli8Francesco Nardi9Department of Life Sciences, University of SienaDepartment of Life Sciences, Imperial College LondonDepartment of Life Sciences, University of SienaDepartment of Life Sciences, University of SienaDepartment of Life Sciences, University of SienaDepartment de Biodiversitat Animal i Microbiana, Institut Mediterrani d’Estudis AvancatsDepartment of Life Sciences, University of SienaDepartment of Life Sciences, University of SienaDepartment of Life Sciences, University of SienaDepartment of Life Sciences, University of SienaComplete mitochondrial genome data are frequently applied to address phylogenetic/phylogeographic issues at different taxonomic levels in ecology and evolution. While sample preparation/sequencing is becoming more and more straightforward thanks to dropping costs for next-generation sequencing (NGS), data preparation and visualization remains a manually intensive step that may lead to errors if improperly conducted. We have elaborated, and here introduce, EZmito, a simple and intuitive, freely accessible Web Server aimed at automating some of these tasks. EZmito is divided into three main tools: EZpipe that assembles DNA matrices for phylo-mitogenomic analyses; EZskew that calculates genome, strand, and codon nucleotide compositional skews and EZcodon which computes Relative Synonymous Codon Usage statistics as well as amino acid usage frequency over multiple mitogenomes. Output is produced in tabular format as well as publication-quality graphics.http://dx.doi.org/10.1080/23802359.2021.1899865web serverphylogenymitogenomenucleotide biasrscu |
| spellingShingle | Claudio Cucini Chiara Leo Nicola Iannotti Sara Boschi Claudia Brunetti Joan Pons Pietro Paolo Fanciulli Francesco Frati Antonio Carapelli Francesco Nardi EZmito: a simple and fast tool for multiple mitogenome analyses Mitochondrial DNA. Part B. Resources web server phylogeny mitogenome nucleotide bias rscu |
| title | EZmito: a simple and fast tool for multiple mitogenome analyses |
| title_full | EZmito: a simple and fast tool for multiple mitogenome analyses |
| title_fullStr | EZmito: a simple and fast tool for multiple mitogenome analyses |
| title_full_unstemmed | EZmito: a simple and fast tool for multiple mitogenome analyses |
| title_short | EZmito: a simple and fast tool for multiple mitogenome analyses |
| title_sort | ezmito a simple and fast tool for multiple mitogenome analyses |
| topic | web server phylogeny mitogenome nucleotide bias rscu |
| url | http://dx.doi.org/10.1080/23802359.2021.1899865 |
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