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Version 3.5 (R2010a) Bioinformatics Toolbox Software

This table summarizes what's new in Version 3.5 (R2010a):

New Features and Changes	Version Compatibility Considerations	Fixed Bugs and Known Problems	Related Documentation at Web Site
Yes Details below	Yes—Details labeled as Compatibility Considerations, below. See also Summary.	Bug Reports Includes fixes	Printable Release Notes: PDF Current product documentation

New and updated features in this version include:

• Data Format and Database Functions

• Pairwise Sequence Alignment Functions

• Multiple Sequence Alignment Functions

• Phylogenetic Tree Tools and Methods

• BioIndexedFile Function, Object, Methods, and Properties

• BioRead Function, Object, Methods, and Properties

• BioMap Function, Object, Methods, and Properties

• Function Elements Being Removed

Data Format and Database Functions

The following functions are new:

• saminfo — Return information about Sequence Alignment/Map (SAM) file.

• samread — Read data from Sequence Alignment/Map (SAM) file.

The following functions are updated:

• fastaread — Read data from FASTA file. Updated to allow trimming of the headers in the output structure by addition of TrimHeaders property.

• fastqread — Read data from FASTQ file. Updated to allow trimming of the headers in the output structure by addition of TrimHeaders property.

• phytreeread — Read phylogenetic tree file. Updated to return a second output containing bootstrap values for tree nodes.

Pairwise Sequence Alignment Functions

The following function is updated:

• fastaread — Read data from FASTA file. Updated to allow trimming of the headers in the output structure by addition of TrimHeaders property.

Multiple Sequence Alignment Functions

The following functions are updated:

• fastaread — Read data from FASTA file. Updated to allow trimming of the headers in the output structure by addition of TrimHeaders property.

• multialign — Align multiple sequences using progressive method. Updated to include a new property, 'UseParallel', which lets you use parfor-loops and compute in parallel mode.

• seqpdist — Calculate pairwise distance between sequences. Updated to include a new property, 'UseParallel', which lets you use parfor-loops and compute in parallel mode.

Compatibility Considerations

In Bioinformatics Toolbox™ Version 3.4 and earlier, the multialign and seqpdist functions included 'JobManager' and 'WaitInQueue' property name/property value pairs, which let you process in parallel, including support for the MATLAB scheduler for clusters.

In Bioinformatics Toolbox Version 3.5, the multialign and seqpdist functions do not include the include the 'JobManager' and 'WaitInQueue' property name/property value pairs. Instead they include the 'UseParallel' property name/property value pair, which lets you process in parallel, including support for:

• Local workers for multicore machines

• The MATLAB scheduler for clusters

• Third-party schedulers for clusters

Phylogenetic Tree Tools and Methods

The following functions are updated:

• phytreeread — Read phylogenetic tree file. Updated to return a second output containing bootstrap values for tree nodes.

• seqpdist — Calculate pairwise distance between sequences. Updated to include a new property, 'UseParallel', which lets you use parfor-loops and compute in parallel mode.

BioIndexedFile Function, Object, Methods, and Properties

Following is a new class for an object that lets you extract information from large multi-entry text files.

• BioIndexedFile — Allow quick and efficient access to large text file with nonuniform-size entries.

This class has properties and methods that are useful for accessing, reading, and parsing data from a large source file.

BioRead Function, Object, Methods, and Properties

Following is a new class for an object that contains data from short-read sequences, including sequence headers, nucleotide sequences, and the quality scores for the sequences.

• BioRead — Contain sequence and quality data.

This class has properties and methods that you can use to explore, access, filter, and manipulate all or a subset of the data, before doing subsequent analyses or sequence alignment and mapping.

BioMap Function, Object, Methods, and Properties

Following is a new class for an object that contains data from short-read sequences, including sequence headers, read sequences, quality scores for the sequences, and data about alignment and mapping to a single reference sequence.

• BioMap — Contain sequence, quality, alignment, and mapping data.

This class has properties and methods that you can use to explore, access, filter, and manipulate all or a subset of the data, before doing subsequent analyses or viewing the data.

Function Elements Being Removed

Function Element Name	What Happens When You Use This Function Element	Use This Instead	Compatibility Considerations
'JobManager' property name/property value pair as input to multialign and seqpdist functions	Warns	'UseParallel' property name/property value pair as input to multialign and seqpdist functions	See the Compatibility Considerations subheading in Multiple Sequence Alignment Functions
'WaitInQueue' property name/property value pair as input to multialign and seqpdist functions	Warns	'UseParallel' property name/property value pair as input to multialign and seqpdist functions	See the Compatibility Considerations subheading in Multiple Sequence Alignment Functions.

Bioinformatics Toolbox Release Notes

Version 3.4 (R2009b) Bioinformatics Toolbox Software

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