Version 2.1 (R14SP2+) Bioinformatics Toolbox™ Software Release Notes

Version 2.1 (R14SP2+) Bioinformatics Toolbox Software

This table summarizes what's new in Version 2.1 (Release 14SP2+)

New features and changes introduced in this version are:

• Sequence Alignment Functions

• Sequence Statistics Functions

• Sequence Utilities Functions

• Phylogenetic Tree Functions

• Phylogenetic Tree Methods

• Microarray Functions

• Statistics Functions

Sequence Alignment Functions

• multialign — Align multiple sequences using a progressive method with Distributed Computing Toolbox™ support.

• multialignread — Read multiple sequence alignment file.

• profalign — Align two profiles using Needleman-Wunsch global alignment.

• showalignment — Updated to show multiply aligned sequences.

• seqpdist — Updated to calculate pairwise distances between observations with Distributed Computing Toolbox support.

Sequence Statistics Functions

• codonbias — Calculate codon frequency for each amino acid in a DNA sequence.

• cpgisland — Locate CpG islands in a DNA sequence.

Sequence Utilities Functions

• rebasecuts — Find restriction enzymes that cut a protein sequence.

• seqtool — Graphical User Interface (GUI) for single sequence analysis.

Phylogenetic Tree Functions

• dnds, dndsml — Estimate synonymous and nonsynonymous substitutions rates.

• seqneighjoin — Reconstruct a phylogenetic tree with a Neighbor-joining method.

Phylogenetic Tree Methods

• getcanonical — Calculate the canonical form of a phylogenetic tree.

• getnewwickstr — Create a Newick formatted string.

• reroot — Change the root of a phylogenetic tree.

• subtree — Extract a subtree.

• weights — Calculate weights for a phylogenetic tree.

Microarray Functions

probesetplot — Plot values for an Affymetrix CHP file probe set.

Statistics Functions

rankfeatures — Renamed function. The previous name was sqtlfeatures.

Version 2.1.1 (R14SP3) Bioinformatics Toolbox Software

Version 2.0.1 (R14SP2) Bioinformatics Toolbox Software