>> help bioinfo
  Bioinformatics Toolbox
  Version 2.4 (R2006b) 03-Aug-2006
 
  File I/O
    affyread         - Read Affymetrix GeneChip files. (Windows only)
    agferead         - Read Agilent Feature Extraction format data.
    blastread        - Read an NCBI BLAST format report file.
    celintensityread - Read probe intensities from Affymetrix CEL files.
    emblread         - Read an EMBL format file.
    fastaread        - Read a sequence from a FASTA format file or URL.
    fastawrite       - Write a sequence to a FASTA format file.
    galread          - Read GenePix GAL file.
    genbankread      - Read a GenBank format file.
    genpeptread      - Read a GenPept format file.
    geosoftread      - Read Gene Expression Omnibus (GEO) SOFT format data.
    getblast         - Get a BLAST report from NCBI.
    getembl          - Get sequence data from EMBL.
    getgenbank       - Get sequence data from GenBank.
    getgenpept       - Get sequence data from GenPept.
    getgeodata       - Get Gene Expression Omnibus (GEO) data.
    gethmmalignment  - Get a multiple alignment from the PFAM database.
    gethmmprof       - Get a HMM from the PFAM database.
    gethmmtree       - Get a phylogenetic tree from the PFAM database.
    getpdb           - Get sequence data from PDB.
    gprread          - Read GenePix GPR file.
    imageneread      - Read ImaGene format results file.
    jcampread        - Read JCAMP-DX file.
    multialignread   - Read a multiple sequence alignment file.
    mzxmlread        - Read mzXML file.
    pdbread          - Read a PDB format file.
    pfamhmmread      - Read a PFAM format HMM profile.
    phytreeread      - Read NEWICK tree formatted file.
    scfread          - Read an SCF format trace file.
    sptread          - Read SPOT format file.
 
  Sequence Conversion
    aa2int          - Convert from amino acid to integer representation.
    aa2nt           - Convert a sequence of amino acids to nucleotides.
    dna2rna         - Convert a sequence of DNA nucleotides to RNA.
    int2aa          - Convert from integer to amino acid representation.
    int2nt          - Convert from integer to nucleotide representation.
    nt2aa           - Convert a sequence of nucleotides to amino acids.
    nt2int          - Convert from nucleotide to integer representation.
    rna2dna         - Convert a sequence of RNA nucleotides to DNA.
    seq2regexp      - Convert a sequence that contains wildcards to a regular expression.
    seqcomplement   - Calculate the complementary strand of a DNA sequence.
    seqrcomplement  - Calculate the reverse complement of a DNA sequence.
    seqreverse      - Reverse a sequence.
 
  Sequence Statistics
    aacount         - Report amino acid counts in a sequence.
    atomiccomp      - Calculate atomic composition of a protein.
    basecount       - Report nucleotide base counts in a sequence.
    codonbias       - Report codon usage per amino acid for a DNA sequence.
    codoncount      - Report codon counts in a sequence.
    cpgisland       - Locate CpG islands in a DNA sequence.
    dimercount      - Report dimer counts in a sequence.
    isoelectric     - Estimate the isoelectric point of a protein sequence.
    molweight       - Calculate molecular weight of a peptide sequence.
    nmercount       - Report n-mer counts in a sequence.
    ntdensity       - Plot nucleotide density along the sequence.
    seqwordcount    - Report word counts for a sequence.
 
  Sequence Utilities
    aminolookup     - Lookup table for peptide symbols.
    baselookup      - Lookup table for nucleotide symbols.
    blastncbi       - Generate a remote NCBI BLAST request.
    cleave          - Cleave a protein with an enzyme.
    featuresmap     - Graphical map showing the features of a GenBank structure.
    featuresparse   - Parse features from GenBank, GenPept, or, EMBL data.
    geneticcode     - Mapping for the genetic code.
    joinseq         - Join two sequences.
    oligoprop       - DNA oligonucleotide sequence properties.
    palindromes     - Find palindromes in a sequence.
    pdbdistplot     - Visualization of inter-molecular distances in a PDB file.
    pdbplot         - Plot 3D backbone structure of proteins in a PDB file.
    proteinplot     - GUI for protein analysis.
    ramachandran    - Ramachandran plot for PDB data.
    randseq         - Generate a random sequence from a finite alphabet.
    rebasecuts      - Find restriction enzymes that cut a sequence.
    restrict        - Split a sequence at a restriction site.
    revgeneticcode  - Reverse mapping for the genetic code.
    seqconsensus    - Compute the consensus sequence for a set of sequences.      
    seqdisp         - Format long sequences for easy viewing.
    seqlogo         - Display sequence logos for DNA and protein sequences.
    seqmatch        - Find matches for every string in a library.
    seqprofile      - Compute the sequence profile of a multiple alignment.
    seqshoworfs     - Graphical display of Open Reading Frames in a sequence.
    seqshowwords    - Graphical display of words in a sequence.
    seqtool         - GUI for sequence analysis.
 
  Sequence Alignment
    multialign       - Progressive multiple sequence alignment.
    multialignviewer - Visualization of multiple sequence alignment.
    nwalign          - Needleman-Wunsch global alignment.
    profalign        - Needleman-Wunsch global alignment of two profiles.
    seqdotplot       - Create a dotplot of two sequences.
    showalignment    - Visualization of pairwise sequence alignment.
    swalign          - Smith-Waterman local alignment.
 
  Statistical Learning
    classify        - Discriminant analysis. (Statistics toolbox)
    classperf       - Evaluate the performance of a classifier.
    crossvalind     - Cross-validation index generation.
    kmeans          - K-means clustering. (Statistics toolbox)
    knnclassify     - K-Nearest neighbor classifier.
    knnimpute       - Impute missing data using the nearest neighbor method.
    randfeatures    - Randomized subset feature selection.
    rankfeatures    - Ranks key features by class separability criteria.
    svmclassify     - Classify using a support vector machine classifier.
    svmtrain        - Train a support vector machine classifier.
    treefit         - Classification tree fitting (Statistics toolbox).
 
  Protein Analysis
    aacount         - Show the amino acid composition of a protein sequence.
    aminolookup     - Lookup table for peptide symbols.
    atomiccomp      - Calculate atomic composition of a protein.
    cleave          - Cleave a protein with an enzyme.
    isoelectric     - Estimate the isoelectric point of a protein sequence.
    molweight       - Calculate molecular weight of a peptide sequence.
    pdbdistplot     - Visualization of inter-molecular distances in a PDB file.
    pdbplot         - Plot 3D backbone structure of proteins in a PDB file.
    proteinplot     - GUI for protein analysis.
    ramachandran    - Ramachandran plot for PDB data.
 
  Trace tools
    scfread         - Read SCF format trace data.
    traceplot       - View nucleotide trace plots.
 
  Profile Hidden Markov Models
    gethmmalignment - Get a multiple alignment from the PFAM database.
    gethmmprof      - Get a HMM from the PFAM database.
    gethmmtree      - Get a phylogenetic tree from the PFAM database.
    hmmprofalign    - Sequence alignment to a profile HMM.
    hmmprofestimate - Estimate the parameters of a profile HMM.
    hmmprofgenerate - Generate a random sequence from a profile HMM.
    hmmprofmerge    - Align the output strings of several profile alignments.
    hmmprofstruct   - Create a profile HMM structure.
    pfamhmmread     - Read a PFAM format HMM profile.
    showhmmprof     - Plot an HMM profile.
 
  Phylogenetic Tree Tools
    dnds            - Estimate synonymous and nonsynonymous substitution rates.
    dndsml          - DNDS using maximum likelihood.
    phytreeread     - Read NEWICK tree formatted file.
    phytreetool     - Interactive tool to explore/edit phylogenetic trees.
    phytreewrite    - Save a phylogenetic tree object as a NEWICK format file.
    seqlinkage      - Construct a phylogenetic tree from pairwise distances.
    seqneighjoin    - Neighbor-joining for phylogenetic tree reconstruction.
    seqpdist        - Pairwise distance between sequences.
 
  Phylogenetic Tree Methods
    phytree              - Phylogenetic tree object.
    phytree/get          - Get information about a phylogenetic tree object.
    phytree/getbyname    - Select branches and leaves by name.
    phytree/getcanonical - Calculates the canonical form of a phylogenetic tree.
    phytree/getnewickstr - Creates a NEWICK formatted string.
    phytree/pdist        - Compute the pairwise patristic distance.
    phytree/plot         - Render a phylogenetic tree.
    phytree/prune        - Reduce a phylogenetic tree by removing branch nodes.
    phytree/reroot       - Changes the root of a phylogenetic tree.
    phytree/select       - Select tree leaves and branches.
    phytree/subtree      - Extracts a subtree.
    phytree/view         - View a phylogenetic tree in phytreetool.
    phytree/weights      - Tree-based sequence weights.
 
  Microarray File Formats
    affyread        - Read Affymetrix GeneChip files. (Windows only)
    agferead        - Read Agilent Feature Extraction format data.
    galread         - Read GenePix GAL file.
    geosoftread     - Read Gene Expression Omnibus (GEO) SOFT format data.
    getgeodata      - Get Gene Expression Omnibus (GEO) data.
    gprread         - Read GenePix GPR file.
    imageneread     - Read ImaGene format results file.
    sptread         - Read SPOT format file.
 
  Microarray Data Analysis and Visualization
    clustergram     - Clustergram plot.
    maboxplot       - Box plot of microarray data.
    maimage         - Pseudocolor plot of microarray spatial data.
    mairplot        - Intensity plot of microarray signals.
    maloglog        - Log-log plot of microarray data.
    mapcaplot       - Principal Component plot of expression profile data.
    mattest         - Unpaired student's t-test of microarray data.
    mavolcanoplot   - Volcano plot of expression profile data.
    redgreencmap    - Generate red and green colormap.
 
  Microarray Normalization and Filtering
    affyinvarsetnorm  - Invariant set normalization of Affymetrix probe-level data.
    exprprofrange     - Calculate range of expression profiles.
    exprprofvar       - Calculate variance of expression profiles.
    geneentropyfilter - Remove genes with entropy expression values.
    genelowvalfilter  - Remove genes with low expression values.
    generangefilter   - Remove genes with small expression ranges.
    genevarfilter     - Remove genes with small expression variance.
    mainvarsetnorm    - Rank invariant set normalization.
    malowess          - Lowess normalization.
    manorm            - Normalization by scaling and centering.
    quantilenorm      - Quantile normalization.
    rmabackadj        - RMA background adjustment of Affymetrix probe-level data.
    rmasummary        - RMA summarization of multiple Affymetrix microarray data.
 
  Microarray Utility Functions
    magetfield        - Extract data from microarray structure.
    probelibraryinfo  - Get library information for a probe.
    probesetlink      - Show probe set information from NetAffx.
    probesetlookup    - Get gene information for a probe set.
    probesetplot      - Plot probe set values.
    probesetvalues    - Get probe set values from CEL and CDF information.
 
  Gene Ontology Functions
    geneont                        - Creates a Gene Ontology (GO) object
    geneont.geneont.getancestors   - Finds the ancestors of a GO term
    geneont.geneont.getdescendants - Finds the descendents of a GO term
    geneont.geneont.getmatrix      - Converts a GO Object into a relationship matrix
    geneont.geneont.getrelatives   - Finds the related terms for a GO term
    goannotread                    - Extract data from microarray structure.
    num2goid                       - Converts numeric values to GO IDs
 
  Mass-Spectrometry Pre-Processing and Visualization
    jcampread         - Read JCAMP-DX file.
    msalign           - Align a spectrum to a set of candidate peaks.
    msbackadj         - Background estimation and correction.
    msheatmap         - Heat map image of a set of spectra.
    mslowess          - Non-parametric smoothing using Lowess method.
    msnorm            - Normalization of a set of spectra.
    msresample        - Resample with antialias filtering.
    mssgolay          - Least-squares polynomial smoothing.
    msviewer          - Plot a spectrum or a set of spectra.
 
  Graph Theory Algorithms
    
    graphallshortestpaths - Find distance of all shortest paths.
    graphconncomp         - Strong and weak connected components.
    graphisdag            - Check if graph is DAG.
    graphisomorphism      - Map between two isomorphic graphs.
    graphisspantree       - Check if graph is a spanning tree.
    graphmaxflow          - Max-flow (and min-cut) algorithm.
    graphminspantree      - Find the minimal spanning tree.
    graphpred2path        - Covert from a predecessor list to a path.
    graphshortestpath     - Find the shortest path between two nodes.
    graphtopoorder        - Topological order of a DAG.
    graphtraverse         - Depth first search and breadth first search.
  
  Graph Visualization Methods
    biograph                           - Create a bioinformatics graph object.
    biograph.biograph.dolayout         - Calculate node and edge positions.
    biograph.biograph.getnodesbyid     - Get handles to nodes.
    biograph.biograph.getedgesbynodeid - Get handles to edges.
    biograph.biograph.view             - Render a graph in its viewer.
    biograph.node.getancestors         - Find ancestors.
    biograph.node.getdescendants       - Find descendants.
    biograph.node.getrelatives         - Find neighbors.
   
  Access to the graph algorithms as a biograph method:
    biograph.biograph.allshortestpaths, biograph.biograph.conncomp,
    biograph.biograph.isdag, biograph.biograph.isomorphism,
    biograph.biograph.isspantree, biograph.biograph.maxflow,
    biograph.biograph.minspantree, biograph.biograph.shortestpath,
    biograph.biograph.topoorder, biograph.biograph.traverse.
    
  Scoring Matrices
    blosum            - BLOSUM family of matrices.
    dayhoff           - Dayhoff matrix.
    gonnet            - Gonnet variation on PAM250.
    nuc44             - Nuc44 nucleotide matrix.
    pam               - PAM family of matrices.
 
  Tutorials, demos and examples.
    affydemo           - Example of working with Affymetrix GeneChip data.
    aligndemo          - Basic sequence alignment tutorial demo. 
    alignscoringdemo   - Tutorial showing the use of scoring matrices. 
    alignsigdemo       - Demo of how to estimate the significance of alignments.
    biclusterdemo      - Clustergram functionality examples.
    biodbdemo          - Example of connecting to local databases.
    biodistcompdemo    - Batch processing through distributed computing.
    biographdemo       - Working with BIOGRAPH objects.
    biojavademo        - Example of calling BioJava functions.
    biomemorymapdemo   - Using memory mapping to work with whole genome data.
    bioperldemo        - Example of calling Bioperl functions.
    biovbscript        - Calling MATLAB from a Web Page using VBScript.
    cancerdetectdemo   - Data mining analysis for mass spectrometry profiles.
    connectkeggdemo    - Connecting to the KEGG API Web Service.
    geneontologydemo   - Example of working with Gene Ontology data.
    hmmprofdemo        - HMM profile alignment tutorial example.
    hivdemo            - Analyzing the origin of the HIV with phylogenetic trees.
    mousedemo          - Microarray normalization and visualization example.
    msgademo           - Mass spectra data analysis with Genetic Algorithms.
    mspreprodemo       - Pre-processing of raw mass spectrometry data.
    phybootdistdemo    - Confidence estimation of trees by bootstrapping.
    primerdemo         - Primer design tutorial example.
    primategeneexpdemo - Analyzing Affymetrix microarray gene expression data
    primatesdemo       - Building a phylogenetic tree for the hominidae species.
    rasmolddedemo      - Connecting to RasMol using DDE on Windows.
    seqstatsdemo       - Sequence statistics tutorial example.
    yeastdemo          - Microarray data analysis example.
 
