Software is classified into off-shelf and self-developed. Most of the off-self software is open source and in public domain. Those software packages are mainly developed in Linux/Unix system, while some can run on both Microsoft Windows and Linux with graphic user interface (GUI). The core facility provides several GUI Bioinformatics packages. In March 2012, we purchased Sequencher 5.0 from Gene Codes Corporation. This is one-user network licensed software. It is mainly used for DNA sequence assembly and analysis for next generation or traditional (Sanger or capillary electrophoresis) DNA data sets. We installed web based general Bioinformatics tool set, EMBOSS Explorer 6.4 (http://virologycenter.unl.edu/emboss-explorer). EMBOSS is the replacement for commercial software package GCG, which is retired years ago. The advantage of EMBOSS Explorer is its accessibility and convenience. Software suite of 454 Sequencing Applications from Roche was installed on our server for analysis of 454 sequence reads. It has three programs GS Amplicon Variant Analyzer, GS De Novo Assembler (also called newbler), and GS Reference Mapper. Users can access the software suite through our server remotely using NX client or directly use the server console in Bioinformatics Core lab. Many command line program packages have been installed and are classified in the following categories.
1. R statistics analysis suite
2. Next generation sequencing data analysis packages
3. Sequence alignment programs ( pairwise and multiple alignments)
4. Phylogenetic analysis programs
5. Transmembrane prediction programs
6. Clustering programs
7. Assembly programs
8. Visualization programs
9. Motif and pattern search and finding
10. Transcription factor binding sites prediction programs
11. Microbiome analysis packages
12. QTL analysis programs
13. Metagenome analysis programs
14. Structure analysis programs