Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Provides string containers, string matching algorithms, and utilities for manipulating large biological sequences or sets of sequences. Biostrings is an R package that uses (1) R external pointers to store the string data, (2) bit patterns to encode the string data, and (3) provides users with a class of objects where each instance can store a set of views on the same big string.
Reads and writes high-throughput sequencing data. The htsfile utility attempts to identify what kind of high-throughput sequencing data files the specified files are, and provides minimal viewing capabilities for some kinds of data file. It can identify sequencing data files such as SAM, BAM, and CRAM; variant calling data files such as VCF and BCF; index files used to index these data files; and compressed versions of many of them.
Offers to users several features to exploit genes and transcripts in general feature format (GFF) through the gene transfer format (GTF2) and GFF3 versions. GFF utilities provides a tool, gffread, for the validation, filtering and converting GFF files. gffcompare is another program that allows the evaluation and comparison of the accuracy of transcript assemblers and the intron/exon coordinates.
A data integration framework for translating fragmented large-scale data into testable predictions. The Anduril framework allows rapid integration of heterogeneous data with state-of-the-art computational methods and existing knowledge in bio-databases. Anduril automatically generates thorough summary reports and a website that shows the most relevant features of each gene at a glance, allows sorting of data based on different parameters, and provides direct links to more detailed data on genes, transcripts or genomic regions. Anduril is open-source; all methods and documentation are freely available.
Provides functions for the import-export of some standard systems biology file formats and a set of algorithms to analyze and reduce the complexity of biological networks. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.