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Contents.m
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% MBEToolbox -- Molecular Biology & Evolution Toolbox (old files)
%
% Data type and file IO
% codonise64 - Codonises sequence(s)
% copyalnheader - Copy header information of an alignment structure into another
% encodeseq - Converts nucleotide from letters to integer
% seqcode - Return matrix for mapping sequence letters to integers
% codontable - Return codon matrix and genetic tables matrix
% readfasta - Reads data from a FASTA formatted file into a MATLAB structure
% readphylip_i - Reads data from an interleaved PHYLIP formatted file
% readphylip_s - Reads data from a sequential PHYLIP formatted file
% printmatrix - Prints to the screen a printout of the matrix
% viewseq - View sequences in alignment
% writefasta - Write alignment structure into a FASTA formatted file
% writephylip_i - Write alignment structure into an interleaved PHYLIP formatted file
% writephylip_s - Write alignment structure into a sequential PHYLIP formatted file
% writematrix - Writes data in tabular form to the file system.
% writeshadedhtml - Write shaded alignment into HTML file
%
% Basic statistic and sequence manipulation
% countntchange - Count nucleotide changes in two DNA sequences
% countaachange - Count amino-acid changes in two protein sequences
% countseqppq - Counts transitions (P1 and P2) and transversion (Q)
% countseqpq - Counts transition (P) and transversion (Q) for the given sequence pair S
% gc4 - Counts GC content at fourfold degenerate sites
% cai - Calculates the Codon Adaptation Index (CAI)
% rscu - Calculates the Relative Synonymous Codon Usage (RSCU) value
% codonusage - Counts codon usage
% codonvolatility - Calculates codon volatility
% countdegeneratesites - Counts degenerate sites in two aligned DNA sequences.
% countinvariablesites - Counts invariable sites.
% ntcomposition - Counts nucleotide composition
% aacomposition - Counts AA composition
% countsegregatingsites - Count segregating sites
% extractdegeneratesites - Extract 0-, 2- and 4-fold degenerate sites
% extractinformativesites - Extract informative sites
% extractinvariablesites - Extract invariable sites
% extractpos - Extract coding position 1, 2, 3 or 1 and 2
% extractsegregatingsites - Extract segregating sites
% getsynnonsyndiff - Return matrices of Syn- Nonsyn- differences between codons
% getsynnonsynsites - Return matrices of Syn- Nonsyn- sites of codons
% hasgap - Check if alignment contains gap
% rmcodongaps - Remove codons with gaps
% rmgaps - Remove gaps in alignment
% revcomseq - Return reverse complement of sequences
% revseq - Return reverse strand of nucleotide sequences
% translatealn - Translate coding DNA sequence into protein sequence in an alignment
% translateseq - Translate coding DNA sequence into protein.
% smithwaterman - Local alignment by Smith & Waterman algorithm
% needlemanwunsch - Gobal alignment of two proteins.
% zscoreprotaln - Z score of protein alignment
% alignseqfile - Align sequence file
% clustalw - Mulitple sequence alignment
% karlinsig - Return the Karlin genomic signatures for a given sequence
% karlinsigdiff - Return the difference of Karlin genomic signatures between two given sequences
% buildpssm - Builds a position specific scoring matrix (PSSM)
% compcomp - Calculates the compositional complexity of sequence
% cataln - Concatenate alignments
% randcut - Cuts genome DNA randomly into shot fragment
%
% Genetic distances
% dc_ng86 - Compute syn. non-syn. substitutions rates by Nei-Gojobori method
% dc_li85 - Compute syn. non-syn. substitutions rates by Li85 method
% dc_li93 - Computes Syn. non-syn. substitutions rates by Li93 method
% dc_ml - Estimate dS and dN by using maximum likelihood algorithm
% dn_ntdiff - Number of different nucleotides and gaps between two sequences
% dn_pdist - p-distances (nucleotide)
% dn_ntfreqdist - Euclidean distances between nucleotide frequencies
% dn_jc - Jukes-Cantor Distance
% dn_k2p - Kimura 80 (2-parameter) Distance
% dn_tajima_nei84 - Tajima & Nei 84 Distance
% dn_tamura92 - Tamura 92 Distance
% dn_f84 - Felsenstain 84 Distance
% dn_hky - Hasegawa, Kishino and Yano 85 (HKY) Distance
% dn_gtr - Distance of GTR model
% dn_jin_nei90 - Jin-Nei Gamma distance
% dn_logdet - Log-det (paralinear) distance
% dn_ntfreqdist - Euclidean distances between nucleotide frequencies
% dp_aadiff - Uncorrected distance of protein sequences
% dp_pdist - p-distances (amino acid)
% dp_poisson - Poisson Correction (PC) distance (amino acid)
% dp_gamma - Gamma distance (amino acids)
% dp_dayhoff - Dayhoff Distance
% dp_jtt - JTT Distance
% dp_wag - WAG Distance
% estimatefreq - Estimates base frequencies of the given sequence(s)
% estimatekappa - Estimates kappa for given sequence pair
% estimateyn00kappa - Estimate transition/transversion rate ratio (kappa) by method of YN00
% gammadistrib - Discrete Gamma model of rate heterogeneity
% invdistrib - Invariable sites model of rate heterogeneity
%
% Phylogeny and likelihood
% mbe_dnaml - M-file for mbe_dnaml.fig
% mbe_dnapars - M-file for mbe_dnapars.fig
% mbe_proml - M-file for mbe_proml.fig
% mbe_protpars - M-file for mbe_protpars.fig
% plotupgma - Performs UPGMA on distance matrix and produces plot of dendrogram
% plotnjtree - Performs neighbor joining (NJ) on distance data and plot NJ tree
% runaddin - Run add-in Phylip commands
% likelidist - Estimates log likelihood of branch length (distance)
% seqpairlikeli - Estimates log-likelihood of branch length (distance)
% likelitree - Estimates log likelihood of a tree
% model_nt - Returns a structure of nucleotide substitution model
% modeljc - Returns a structure of model JC
% modelk2p - Returns a structure of model K2P
% modelf81 - Returns a structure of model F81
% modelhky - Returns a structure of model HKY
% modelgtr - Returns a structure of model GTR
% model_aa - Returns a structure of amino-acid substitution model
% modeldayhoff - Returns a structure of model Dayhoff
% modeljtt - Returns a structure of model JTT
% modelwag - Returns a structure of model WAG
% randtre - Generates a random tree with n OTUs
% readnewick - Reads tree from standart file in Newick format
% sitepattern - Infers site patterns for a given alignment
% optimlikelidist - Optimises distance of given sequence pair under a model
% optimlikelidistk2p - Optimises distance and kappa under a K2P model
% optimseqpairlikeli - Optimises distance of given sequence pair under a model
% parsetree - Parses string of tree in Newick format
% composeQ - Computes normalized rate matrix Q from R matrix (general reversible model)
% compequtest - Compositional equilibrium test
%
% Graph and plot
% plotcorresp - Performs correspondence analysis and plot result
% plotdiplomo - Plot DiPloMo graph
% plotdistvstrans - Plot genetic distances (NG86) vs. transitions and transversions
% plotkavsks - Plot Ka vs. Ks
% plotntcomposition - Plot nucleotide composition
% plotslidingwin - Performs sliding window analysis on a nucleotide sequence
% plotslidingwinkaks - Plot cumulative Ka and Ks curves
% plotzcurve - Z curve plotter
% zcurve - Return Z curve components
%
% Polymorphism
% reportpolysites - Report polymorphic sites
% tajima89test - Tajima's Test of Neutrality
% MBEGUI - MBEToolbox GUI
% MBEDEMO - DEMO1: Alignment file IO
% - DEMO2: Basic sequence statistics
% - DEMO3: Genetic distances estimation
% - DEMO4: Phylogenetic inferences
%
%% $Date: 2013-01-05 12:04:29 -0600 (Sat, 05 Jan 2013) $