Google core libraries for Java

Implementation of various string similarity and distance algorithms: Levenshtein, Jaro-winkler, n-Gram, Q-Gram, Jaccard index, Longest Common Subsequence edit distance, cosine similarity ...

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

The Chemistry Development Kit

Java utilities for Bioinformatics

Automatically exported from code.google.com/p/figtree

Graphstream core

Similarity or Distance Metrics, e.g. Levenshtein, for Java

A fast and easy to use decision tree learner in java

Chemical 2D structure editor application/applet based on the Chemistry Development Kit

Reaction Decoder Tool (RDT) - Atom Atom Mapping Tool

Java Natural Order comparator

SMSD — exact substructure & MCS search for chemical graphs.

Refactored libsvm for easily plugging custom kernels (e.g., Tree Kernel) written in Java.

Perception and labelling of stereogenic centres in chemical structures

Essential Cheminformatics

MzidLib - A library of routines for manipulating data in the PSI's mzIdentML standard.

JChemPaint

Minimum/Maximum Spanning Tree (MST) algorithm for directed and undirected graphs

Sample code for canonical labelling of graphs

Orbital Development Kit

This is a hashed fingerprint based on the shortest path. The idea is to skip the exhaustive path based finger printers where the runtime is exponential.

General vector-drawing framework

How to run SMSD using Java Threads

Improvised CDK Hashed fingerprint

Automatically exported from code.google.com/p/fast-random-forest

The Chemistry Development Kit

Union of two molecules

Substructure code benchmarking