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TOPALi v2

Biomathematics and Statistics Scotland. Statistical and evolutionary analysis of multiple sequence alignments. Nov 2008: We now have a new TOPALi publication in Bioinformatics:. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Version 2" of TOPALi is a complete overhaul to the original TOPALi. Analyses methods that used to run locally within TOPALi can now optionally run remotely on high-performance compute clusters.

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TOPALi v2 | topali.org Reviews

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Biomathematics and Statistics Scotland. Statistical and evolutionary analysis of multiple sequence alignments. Nov 2008: We now have a new TOPALi publication in Bioinformatics:. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Version 2 of TOPALi is a complete overhaul to the original TOPALi. Analyses methods that used to run locally within TOPALi can now optionally run remotely on high-performance compute clusters.

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1 topali v2

2 topali v2 homepage

3 download topali v2

4 screenshots

5 publications

6 world map

7 our software

8 curlywhirly

9 flapjack

10 optiras

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TOPALi v2 | topali.org Reviews

https://topali.org

Biomathematics and Statistics Scotland. Statistical and evolutionary analysis of multiple sequence alignments. Nov 2008: We now have a new TOPALi publication in Bioinformatics:. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Version 2" of TOPALi is a complete overhaul to the original TOPALi. Analyses methods that used to run locally within TOPALi can now optionally run remotely on high-performance compute clusters.

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topali.org

1

TOPALi v2 Screenshots

http://www.topali.org/screenshots.shtml

Biomathematics and Statistics Scotland. The main TOPALi interface, showing alignment handling and overview windows:. Monitoring and tracking the progress of multiple concurrent job submissions (running both locally and remotely on a cluster):. Graphical results from a Hidden Markov Model (HMM) recombination detection run:. Various phylogenetic trees that have been generated within TOPALi:. Determinging the inputs and settings for a new HMM job submission:. Biomathematics and Statistics Scotland.

2

TOPALi v2

http://www.topali.org/index.shtml

Biomathematics and Statistics Scotland. Statistical and evolutionary analysis of multiple sequence alignments. Nov 2008: We now have a new TOPALi publication in Bioinformatics:. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Version 2" of TOPALi is a complete overhaul to the original TOPALi. Analyses methods that used to run locally within TOPALi can now optionally run remotely on high-performance compute clusters.

3

Publications

http://www.topali.org/publications.shtml

Biomathematics and Statistics Scotland. Selected publications related to this work, include:. Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF and Wright F (2008), TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 25 (1), 126-127. View PDF. Husmeier D, Wright F and Milne I (2005), Detecting interspecific recombination with a pruned probabilistic divergence measure.

4

TOPALi

http://www.topali.org/topali-v1

TOPALi provides an intuitive graphical interface for working with existing statistical methods designed for detecting recombination in DNA sequence alignments. Once recombinant regions have been identified, further (automated if desired) analysis is then possible, including the creation of Phylogenetic trees, mosaic structure predictions, and HTML report generation. TOPALi has now been superceded by TOPALi v2. Click here for details. Current version is 0.28, released 21st Nov 2005. View the mosaic struct...

5

Download TOPALi v2

http://www.topali.org/download.shtml

Biomathematics and Statistics Scotland. TOPALi is compatible with Microsoft Windows, Apple Mac OS X, and Linux. Please choose the most appropriate installer for your system from the list below. Mac OS X Installer. The source code for TOPALi is publically available via Subversion at the following URL: http:/ ics.hutton.ac.uk/svn/topali-v2. Biomathematics and Statistics Scotland.

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ics.hutton.ac.uk

Helium : Information & Computational Sciences

https://ics.hutton.ac.uk/helium

Web Sites & Databases. Tools, Libraries & Scripts. Working Together For Better Outcomes (2015). Information and Computational Sciences. Helium Pedigree Visualization Framework. We are pleased to announce that Helium is n ow available for download. Helium allows, in this case barley DUS characters, to be colour coded and viewed in a pedigree context. Helium won best paper award at BioVis 2014 in Boston, USA. BMC Bioinformatics. 15:259. DOI: 10.1186/1471-2105-15-259. From the Institute for Informatics and ...

ics.hutton.ac.uk

Tablet : Information & Computational Sciences

https://ics.hutton.ac.uk/tablet

Web Sites & Databases. Tools, Libraries & Scripts. Working Together For Better Outcomes (2015). Information and Computational Sciences. Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. Page to get the latest version of Tablet (1.16.09.06; 6th September 2016). Briefings in Bioinformatics 14(2), 193-202. High-performance visualization and data navigation. Display of reads in both packed and stacked formats. Germinate 3 Data Importer. Experti...

ics.hutton.ac.uk

Flapjack : Information & Computational Sciences

https://ics.hutton.ac.uk/flapjack

Web Sites & Databases. Tools, Libraries & Scripts. Working Together For Better Outcomes (2015). Information and Computational Sciences. Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, allowing for rapid navigation and comparisons between lines, markers and chromosomes. Page to get the latest version of Flapjack (1.16.10.31; 31st October 2016). All results are saved in a Flapjack project format file and can also be exported as raw data or gra...

ics.hutton.ac.uk

Desktop Applications : Information & Computational Sciences

https://ics.hutton.ac.uk/software/desktop-applications

Web Sites & Databases. Tools, Libraries & Scripts. Working Together For Better Outcomes (2015). Information and Computational Sciences. With the odd exception, the desktop applications produced by the ICS group are available across a range of platforms and are designed to be both easy-to-use and easy-to-deploy. We provide simple installers (via the excellent install4j. Suite) that bundle both the application and any of its dependencies in a single package. Http:/ ics.hutton.ac.uk/humbug. CurlyWhirly is a...

ics.hutton.ac.uk

CurlyWhirly : Information & Computational Sciences

https://ics.hutton.ac.uk/curlywhirly

Web Sites & Databases. Tools, Libraries & Scripts. Working Together For Better Outcomes (2015). Information and Computational Sciences. CurlyWhirly is an application for viewing multi-dimensional data, with a particular focus on the outputs of Principle Coordinate Analysis and Principal Components Analysis. Page to get the latest version of CurlyWhirly 1.16.05.26. 3D display of multi-dimensional data. Rotate the graph by dragging on the display. Zoom in and out of the data set. Germinate 3 Data Importer.

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TOPALi v2

Biomathematics and Statistics Scotland. Statistical and evolutionary analysis of multiple sequence alignments. Nov 2008: We now have a new TOPALi publication in Bioinformatics:. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Version 2" of TOPALi is a complete overhaul to the original TOPALi. Analyses methods that used to run locally within TOPALi can now optionally run remotely on high-performance compute clusters.

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