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An interactive viewer for large phylogenetic trees and networks: All [22] DensiTree A viewer capable of viewing multiple overlaid trees. All [23] FigTree: Simple Java tree viewer able to read newick and nexus tree files. Can be used to color branches and produce vector artwork. All [24] JEvTrace
Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using Archaeopteryx: Software is package of 7 interactive visual tools for multiple sequence alignments. Major focus is manipulating large alignments. Includes MSApad, MSA comparator, MSA reconstruction tool, FASTA generator and MSA ID matrix calculator
Archaeopteryx is an interactive computer software program, written in Java, for viewing, editing, and analyzing phylogenetic trees.This type of program can be used for a variety of analyses of molecular data sets, but is particularly designed for phylogenomics.
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 [25 ...
SplitsTree is a popular freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, splits graphs, from various types of data such as a sequence alignment, a distance matrix or a set of trees.
It uses a basic tree structure to organize information, and allows the user to define different types of nodes and leaves. File formats ... Mobile view ...
JSON: No Smile Format Specification: Yes No Yes Partial (JSON Schema Proposal, other JSON schemas/IDLs) Partial (via JSON APIs implemented with Smile backend, on Jackson, Python) — SOAP: W3C: XML: Yes W3C Recommendations: SOAP/1.1 SOAP/1.2: Partial (Efficient XML Interchange, Binary XML, Fast Infoset, MTOM, XSD base64 data) Yes Built-in id ...
JSON Schema specifies a JSON-based format to define the structure of JSON data for validation, documentation, and interaction control. It provides a contract for the JSON data required by a given application and how that data can be modified. [ 29 ]