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Algorithm and program for comparing primary biological sequence information, including DNA and protein sequences. Cross-platform: Public domain: National Center for Biotechnology Information: CP2K: Perform atomistic simulations of solid state, liquid, molecular and biological systems, written in Fortran 2003. ? GPL and LGPL: Free open source ...
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 Unknown Unknown No C++ PlantUML, Mermaid.js Generate PlantUML and Mermaild.js diagrams from existing C++ codebase. Dia: Partly No No No
Software suite to search and cluster huge sequence sets. Similar sensitivity to BLAST and PSI-BLAST but orders of magnitude faster: Protein: Steinegger M, Mirdita M, Galiez C, Söding J [10] 2017 USEARCH Ultra-fast sequence analysis tool: Both: Edgar, R. C. (2010). "Search and clustering orders of magnitude faster than BLAST". Bioinformatics.
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.
This is a list of free and open-source software packages, computer software licensed under free software licenses and open-source licenses.Software that fits the Free Software Definition may be more appropriately called free software; the GNU project in particular objects to their works being referred to as open-source. [1]
Results of differential expression analysis can be integrated with ChIP-Seq data to build average tag density profiles and heat maps. The package makes use of several tools open source tools including STAR and DESeq. See also. [72] Chipster is a user-friendly analysis software for high-throughput data. It contains over 350 analysis tools for ...
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.
A program for predicting unique local RNA structures in large sequences with unusually stable folding. 1: None: Yes: sourcecode webserver [153] Xrate: a program for analysis of multiple sequence alignments using phylogenetic grammars, that may be viewed as a flexible generalization of the "Evofold" program. any: Yes: Yes: sourcecode [97] Notes