| Version 1.1 (R14) Bioinformatics Toolbox™ Software Release Notes | |
This table summarizes what's new in Version 1.1 (Release 14)
| New Features and Changes | Version Compatibility Considerations | Fixed Bugs and Known Problems | Related Documentation at Web Site |
|---|---|---|---|
| Yes Details below | No | No bug fixes | No |
New features and changes introduced in this version are
New functions for phylogenetic tree creation and analysis.
phytreeread — Read a Newick-formatted tree file into the MATLAB workspace and return a phytree object with data from the file. Data in the file uses the Newick (New Hampshire) format for describing trees.
phytreewrite — Copy the contents of a phytree object from the MATLAB workspace to a file.
phytreetool — Interactive GUI that allows you to view, edit, and explore phylogenetic tree data. This GUI allows branch pruning, reordering, renaming, and distance exploring. It can also open or save Newick-formatted files.
seqlinkage — Construct a phylogenetic tree from pairwise distances.
seqpdist — Calculate the pairwise distance between biological sequences.
New object for manipulating phylogenetic tree data.
phytree — Function to create a phytree object.
get — Get property values from a phytree object
getbyname — Get node names from a phytree object.
pdist — Calculate the patristic distances between pairs of leaf nodes.
plot — Draw a phylogenetic tree object in a MATLAB Figure window as a phylogram, cladogram, or radial tree.
prune — Remove nodes from a phylogenetic tree.
select — Select branches and leaves from a phylogenetic tree using a specified criteria.
view — Open a phylogenetic tree in a phytreetool window.
Updated Hidden Markov Model profile functions.
The model structure that HMM functions use now includes loop and null transition probabilities. You can read null and loop probabilities from PFAM files using pfamhmmread, and, from PFAM Web databases, using gethmmprof.
When the function hmmprofstruct builds an HMM model, the loop and null transition probabilities default to predefined values. If necessary, you can later modify the probabilities using the same function.
hmmprofalign includes two new properties to control the scoring of flanking states and null transition probabilities. In addition, a third output argument with indices pointing to the respective symbols of the query sequence was added.
blastncbi, blastread, getblast — BLAST sequences and view results from within the MATLAB software.
imageneread — Read microarray data from an ImaGene® Results file.
affyread — Read microarray data from Affymetrix GeneChip files.
gprread — Read microarray data from GenePix® Results (GPR) files.
mapcaplot — Create a Principal Component plot of expression profile data.
clustergram — Updated function to do two way bi-clustering.
isoelectric — Estimate the isoelectric point (the pH at which the protein has a net charge of zero) for an amino acid sequence and estimate the charge for a given pH.
seqdisp — Formats sequence output for easy viewing.
seqmatch — Find matches for every string in a library.
seqdotplot — Updated function now returns a second output (the matrix of matches as a sparse matrix).
aminolookup , baselookup — Updated functions to get IUB/UPAC character codes, integer codes, and names for nucleotides and amino acids.
Bicluster demo — Demonstrates some of the options of the clustergram function.
Bioperl demo — Illustrates the interoperability between the MATLAB software and Bioperl, passing arguments from the MATLAB software to Perl scripts and pulling BLAST search data back to the MATLAB software.
Phytree demo for Hominidae species— A phylogenetic tree is constructed from mtDNA sequences for the Hominidae taxa (also known as pongidae). This family embraces the gorillas, chimpanzees, orangutans and the humans.
Phytree demo for HIV/SIV — Analyzes the reconstruction of phylogenetic trees from infected HIV/SIV organisms.
| Version 1.1.1 (R14SP1) Bioinformatics Toolbox Software | Version 1.0 (R13+) Bioinformatics Toolbox Software | |
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