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an online tool for phylogenetic tree view (newick format) that allows multiple sequence alignments to be shown together with the trees (fasta format) EvolView [3] an online tool for visualizing, annotating and managing phylogenetic trees IcyTree [4] Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks
Microsoft Azure DevOps, Jira, Requirements.cc, Excel, Word Provides management of actors, use cases, user stories, declarative requirements, and test scenarios. Includes glossary, data dictionary, and issue tracking. Supports use case diagrams, auto-generated flow diagrams, screen mock-ups, and free-form diagrams. clang-uml: Unknown Unknown
The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
PlantUML is an open-source tool allowing users to create diagrams from a plain text language. Besides various UML diagrams, PlantUML has support for various other software development related formats (such as Archimate, Block diagram, BPMN, C4, Computer network diagram, ERD, Gantt chart, Mind map, and WBD), as well as visualisation of JSON and YAML files.
General-purpose freeware diagram editor; Can be used to draw different kinds of diagrams: flowcharts, computer network diagrams, UML diagrams, BPMN diagrams, mind maps, organization charts, entity relationship diagrams and many others; Mind42: Proprietary: Mind mapping: Web browser: Yes Yes Yes Browser-based collaborative web application
Dia has special objects to help draw entity-relationship models, Unified Modeling Language (UML) diagrams, flowcharts, network diagrams, and simple electrical circuits. It is also possible to add support for new shapes by writing simple XML files, using a subset of Scalable Vector Graphics (SVG) to draw the shape.
The extensible NEXUS file format is widely used in phylogenetics, evolutionary biology, and bioinformatics.It stores information about taxa, morphological character states, DNA and protein sequence alignments, distances, and phylogenetic trees. [1]
diagrams.net (previously draw.io [2] [3]) is a cross-platform graph drawing software application developed in HTML5 and JavaScript. [4] Its interface can be used to create diagrams such as flowcharts , wireframes , UML diagrams, organizational charts , and network diagrams .