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      GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

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          Abstract

          Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static “GrapeTree Layout” algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.

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          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Alexandros Stamatakis (2014)
          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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            TreeView: an application to display phylogenetic trees on personal computers.

            R D Page (1996)
            Article 0 comments Cited 1225 times – based on 0 reviews     Review now
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              Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

              Ivica Letunic, Peer Bork (2016)
              Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. Finally, iTOL's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users.
              Article 0 comments Cited 1021 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Res
                Journal ID (iso-abbrev): Genome Res
                Journal ID (hwp): genome
                Journal ID (pmc): genome
                Journal ID (publisher-id): GENOME
                Title: Genome Research
                Publisher: Cold Spring Harbor Laboratory Press
                ISSN (Print): 1088-9051
                ISSN (Electronic): 1549-5469
                Publication date (Print): September 2018
                Publication date PMC-release: September 2018
                Volume: 28
                Issue: 9
                Pages: 1395-1404
                Affiliations
                [1 ]Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom;
                [2 ]Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), 1000-029 Lisboa, Portugal;
                [3 ]ADEETC, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, 1959-007 Lisboa, Portugal;
                [4 ]Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
                [5 ]Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-004 Lisboa, Portugal
                Author notes
                Author information
                http://orcid.org/0000-0001-9783-0366
                http://orcid.org/0000-0002-1243-0767
                http://orcid.org/0000-0001-8112-7027
                http://orcid.org/0000-0001-6074-3074
                http://orcid.org/0000-0001-6815-0070
                Article
                Medline ID: 9509184
                DOI: 10.1101/gr.232397.117
                PMC ID: 6120633
                PubMed ID: 30049790
                SO-VID: 803dfcec-50a9-4185-9bac-865dfdd265c6
                Copyright © © 2018 Zhou et al.; Published by Cold Spring Harbor Laboratory Press
                License:

                This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 14 November 2017
                Date accepted : 24 July 2018
                Page count
                Pages: 10
                Funding
                Funded by: Wellcome Trust , open-funder-registry 10.13039/100010269;
                Award ID: 202792/Z/16/Z
                Categories
                Subject: Method

                Data availability:

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