Here is (one of many possible) tables of software data:
| Name | Summary | Bio Tags | Meth Tags | Features | Language | Licence | OS |
|---|---|---|---|---|---|---|---|
| .NET BIO | ".NET Bio is an open source library of common bioinformatics functions, intended to simplify the creation of life science applications. The core library implements a range of file parsers and formatters for common file types, connectors to commonly-used web services such as NCBI BLAST, and standard algorithms for the comparison and assembly of DNA, RNA and protein sequences. Sample tools and code snippets are also included." | Sequence analysis | Windows Linux | ||||
| 4peaks | Allows viewing sequencing trace files, motif searching trimming, BLAST and exporting sequences. | Sequencing | Sequence analysis | Freeware | Mac OS X | ||
| A5 | A5 is an integrative pipeline for genome assembly that automates sequence data cleaning, error correction, assembly, and quality control by chaining a number of programs together with additional custom algorithms. | Sequence assembly | De-novo assembly | GPLv3 | Linux Mac OS X | ||
| AB Large Indel Tool | Identifies deviations in clone insert size that indicate intra-chromosomal structural variations compared to a reference genome. | Indel detection Sequencing | Mapping | GPL | Linux 64 | ||
| AB Small Indel Tool | The SOLiD™ Small Indel Tool processes the indel evidences found in the pairing step of the SOLiD™ System Analysis pipeline Tool (Corona Lite). | Indel detection Sequencing | Read mapping Sequence alignment | GPL | Linux 64 | ||
| ABBA | Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly | Sequence assembly | Sequence assembly Scaffolding | Artistic License | Linux | ||
| ABMapper | Maps RNA-Seq reads to target genome considering possible multiple mapping locations and splice junctions | Genomics Transcriptomics | Read mapping Sequence alignment | GPLv3 | Linux | ||
| ABySS | ABySS is a de novo sequence assembler designed for short reads and large genomes. | Sequence assembly (de novo assembly) | Sequence assembly Sequence assembly (de-novo assembly) | MPI OpenMP | Commercial Freeware | POSIX Linux Mac OS X | |
| Adapter Removal (software) | Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format. | Workflows | Adapter removal | Sequence trimming | Custom Licence | Linux 64 Windows Mac OS X | |
| ADTEx | Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples. | Copy number estimation Exome analysis Cancer biology Next Generation Sequencing | Statistical calculation | Copy number analysis | GPLv3 | GNU/Linux | |
| AGE | AGE is a tool that implements an algorithm for optimal alignment of sequences with SVs. | Structural variation | Sequence alignment | Creative Commons license (Attribution-NonCommerical). | |||
| AGILE | A hash table based high throughput sequence mapping algorithm for longer 4A54 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process | Mapping | |||||
| Agp2amos | missing | Formatting | Windows Linux | ||||
| Alcovna | ALgorithms for COmparing and Visualizing Non Assembled data | SNP detection | |||||
| ALEXA-Seq | Alternative Expression Analysis by massively parallel RNA sequencing | RNA-Seq quantification Alternative splicing | GPLv3 | ||||
| ALLPATHS | De novo assembly of whole-genome shotgun microreads. | Sequence assembly (de novo assembly) | Sequence assembly Sequence assembly (de-novo assembly) | ||||
| Alta-Cyclic | Alta-Cyclic is a Illumina Genome-Analyzer (Solexa) base caller. | Base-calling | |||||
| AMOS | AMOS is a Modular, Open-Source whole genome assembler. | Sequence assembly Sequence assembly validation Integrated solution Formatting Sequence assembly visualisation | Linux | ||||
| ANCHOR | Post-processing tools for de novo assemblies | De-novo assembly | Sequence assembly | BCCA (academic use) | Linux | ||
| AnCorr | Webserver/tool for evaluation coordinate and ordinal correlations between genomic tracks and/or expression or protein binding profiles. | Genomics | Statistical calculation Correlation | Easy-to-use point-and-click web interface with context help | free for non-commercial academic research | Cross-Platform | |
| ... further results | |||||||