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MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien Mozziconacci [28 ...
Extensive data warehouse system for the analysis and integration of biological datasets written in Java and JavaScript Cross-platform: LGPL: University of Cambridge: LabKey Server: Software platform, allows organizations to integrate, analyze, and share complex biomedical data Linux, macOS, Windows: Apache: LabKey Software Foundation LAMMPS
Databases for oncogenomic research are biological databases dedicated to cancer data and oncogenomic research. They can be a primary source of cancer data, offer a certain level of analysis (processed data) or even offer online data mining.
a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and ...
A related project is LinguaPhylo (LPhy). [5] LPhy is a probabilistic programming language for defining phylogenetic analyses with a syntax similar to OpenBUGS.It provides a way to generate BEAST 2 XML files (and similar model specifications for other phylogenetics packages) without needing to write the XML by hand.
The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography. [3] [4] [5] Molecular phylogenetics and molecular evolution correlate. Molecular evolution is the process ...
A phylogenetic tree in MEGA using a Neighbor Joining Method and Bootstrapping. The data sequences being used is from the study Initial diversification of living amphibians predated the breakup of Pangaea. MEGA has created captions using the Real-Time Caption Editor to be able to analyze the properties of the results of the phylogenetic tree.
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.