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- Description:
Sequence analysis is one of the major subjects of bioinformatics. Several existing libraries combine the representation of biological sequences with exact and approximate pattern matching as well as alignment algorithms. We present Jstacs, an open source Java library, which focuses on the statistical analysis of biological sequences instead. Jstacs comprises an efficient representation of sequence data and provides implementations of many statistical models with generative and discriminative approaches for parameter learning. Using Jstacs, classifiers can be assessed and compared on test datasets or by cross-validation experiments evaluating several performance measures. Due to its strictly object-oriented design Jstacs is easy to use and readily extensible.
- Changes to previous version:
New classes and packages:
- Jstacs 2.3 is the first release to be accompanied by JstacsFX, a library for building JavaFX-based graphical user interfaces based on JstacsTools
- new interface MultiThreadedFunction
- new class LargeSequenceReader for reading large sequence files in chunks
- new interface QuickScanningSequenceScore
- new class RegExpValidator for checking String inputs against a regular expression
- new class IUPACDNAAlphabet
New features and improvements:
- Alignments may now handle different costs for insert and delete gaps
- ListResults may now be constructed from Collections of ResultSets
- Several minor improvements and bugfixes in many classes
- Improvements of documentation of several classes
- BibTeX Entry: Download
- Corresponding Paper BibTeX Entry: Download
- Supported Operating Systems: Cygwin, Linux, Macosx, Windows, Unix, Agnostic, Solaris, Freebsd, Platform Independent
- Data Formats: Plain Ascii, Fasta
- Tags: Bioinformatics, R, Classification, Machine Learning, Bayesian Networks, Markov Random Fields, Supervised Learning, Em, Mixture Models, Java, Learning Principles, Probabilistic Models, Motif Discovery
- Archive: download here
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