Standard operating procedure for computing pangenome trees

We present the pan-genome tree as a tool for visualizing similarities and differences between closely related microbial genomes within a species or genus. Distance between genomes is computed as a weighted relative Manhattan distance based on gene family presence/absence. The weights can be chosen w...

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Detalles Bibliográficos
Autores principales: Snipen, Lars, Ussery, David W.
Formato: Texto
Lenguaje:English
Publicado: Michigan State University 2010
Materias:
Standard Operating Procedures
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035256/
https://www.ncbi.nlm.nih.gov/pubmed/21304685
http://dx.doi.org/10.4056/sigs.38923
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author Snipen, Lars
Ussery, David W.
author_facet Snipen, Lars
Ussery, David W.
author_sort Snipen, Lars
collection PubMed
description We present the pan-genome tree as a tool for visualizing similarities and differences between closely related microbial genomes within a species or genus. Distance between genomes is computed as a weighted relative Manhattan distance based on gene family presence/absence. The weights can be chosen with emphasis on groups of gene families conserved to various degrees inside the pan-genome. The software is available for free as an R-package.
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spelling pubmed-30352562011-02-08 Standard operating procedure for computing pangenome trees Snipen, Lars Ussery, David W. Stand Genomic Sci Standard Operating Procedures We present the pan-genome tree as a tool for visualizing similarities and differences between closely related microbial genomes within a species or genus. Distance between genomes is computed as a weighted relative Manhattan distance based on gene family presence/absence. The weights can be chosen with emphasis on groups of gene families conserved to various degrees inside the pan-genome. The software is available for free as an R-package. Michigan State University 2010-01-28 /pmc/articles/PMC3035256/ /pubmed/21304685 http://dx.doi.org/10.4056/sigs.38923 Text en http://creativecommons.org/licenses/by/2.5/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Standard Operating Procedures
Snipen, Lars
Ussery, David W.
Standard operating procedure for computing pangenome trees
title Standard operating procedure for computing pangenome trees
title_full Standard operating procedure for computing pangenome trees
title_fullStr Standard operating procedure for computing pangenome trees
title_full_unstemmed Standard operating procedure for computing pangenome trees
title_short Standard operating procedure for computing pangenome trees
title_sort standard operating procedure for computing pangenome trees
topic Standard Operating Procedures
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035256/
https://www.ncbi.nlm.nih.gov/pubmed/21304685
http://dx.doi.org/10.4056/sigs.38923
work_keys_str_mv AT snipenlars standardoperatingprocedureforcomputingpangenometrees
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