Bioinformatics Toolbox 4.0

Latest Features

Version 4.0

Released: 1 Sep 2011
 

Version 4.0, an update to Release 2011b, includes the following enhancements:

• NGS Browser for viewing and investigating multiple tracks of SAM- or BAM-formatted data and feature annotations
• Objects and methods for managing GFF and GTF feature annotations
• NGS workflow demos including ChIP-Seq and RNA-Seq
• BioMap object for indexed access to both SAM- and BAM-formatted files

See the Release Notes for details.

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Version 3.8

Released: 21 Apr 2011
 

Version 3.8, an update to Release 2011a, includes the following enhancements:

• Browser for Next Generation Sequencing data
• NGS workflow demos, including ChiP-Seq and RNA-Seq

See the Release Notes for details.

Version 3.7

Released: 8 Apr 2011
 

Version 3.7, part of Release 2011a, includes the following enhancements:

• High resolution (pileup) and binned coverage calculations for NGS data sets
• Efficient counting algorithms based on effective alignment for NGS data sets
• Performance improvement and less memory footprint for operations on mapped short reads
• BioMap and BioIndexedFile subsettingmethods to handle NGS data sets with multiple references and to efficiently filter data sets

See the Release Notes for details.

Version 3.6

Released: 3 Sep 2010
 

Version 3.6, part of Release 2010b, includes the following enhancements:

• Support for CIGAR strings for sequence mapping and alignment
• Indexed file access to BAM-formatted files
• Ability to read Bowtie- and SOAP-formatted files

See the Release Notes for details.

Version 3.5

Released: 5 Mar 2010
 

Version 3.5, part of Release 2010a, includes the following enhancements:

• Data representation for next-generation sequencing reads and alignments in MATLAB
• Indexed file access to next-generation sequencing file formats, such as SAM and FASTQ
• Support for reading large text files, such as annotation files
• Expanded parallel computing support in phylogenetic tree reconstruction and multiple alignments, including local workers for multi-core machines and third-party schedulers for clusters

See the Release Notes for details.

Version 3.4

Released: 4 Sep 2009
 

Version 3.4, part of Release 2009b, includes the following enhancements:

• Expanded next-generation sequencing support, including optimized short-read sequence alignment and the reading and writing of common file formats, such as FASTQ and SFF files
• New objects for storing microarray experimental results and annotations
• New heatmap visualization object with annotation support
• Enhanced visualizations for unrooted phylogenetic trees and clustergrams
• New method for cluster validation of phylogenetic trees
• New function for calculating high-resolution isotopic mass distribution

See the Release Notes for details.