Documentation 
Calculate pairwise distance between sequences
D = seqpdist(Seqs)
D = seqpdist(Seqs,
...'PropertyName', PropertyValue,
...)
D = seqpdist(Seqs,
...'Method', MethodValue, ...)
D = seqpdist(Seqs,
...'Indels', IndelsValue, ...)
D = seqpdist(Seqs,
...'OptArgs', OptArgsValue, ...)
D = seqpdist(Seqs,
...'PairwiseAlignment', PairwiseAlignmentValue,
...)
D = seqpdist(Seqs,
...'UseParallel', UseParallelValue, ...)
D = seqpdist(Seqs,
...'SquareForm', SquareFormValue ...)
D = seqpdist(Seqs,
...'Alphabet', AlphabetValue, ...)
D = seqpdist(Seqs,
...'ScoringMatrix', ScoringMatrixValue, ...)
D = seqpdist(Seqs,
...'Scale', ScaleValue, ...)
D = seqpdist(Seqs,
...'GapOpen', GapOpenValue, ...)
D = seqpdist(Seqs,
...'ExtendGap', ExtendGapValue, ...)
Seqs  Any of the following:
 
MethodValue  String that specifies the method to calculate pairwise distances. Default is 'JukesCantor'.  
IndelsValue  String that specifies how to treat sites with gaps. Default is 'score'.  
OptArgsValue  String or cell array that specifies one or more input arguments required or accepted by the distance method specified by the Method property.  
PairwiseAlignmentValue  Controls the global pairwise alignment of input sequences (using
the nwalign function), while
ignoring the multiple alignment of the input sequences (if any). Choices
are true or false. Default is:
 
UseParallelValue  Controls the calculation of the pairwise distances using parforloops. When true, and Parallel Computing Toolbox™ is installed and a parpool is open, computation occurs in parallel. If there are no open parpool, but automatic creation is enabled in the Parallel Preferences, the default pool will be automatically open and computation occurs in parallel. If Parallel Computing Toolbox is installed, but there are no open parpool and automatic creation is disabled, then computation uses parforloops in serial mode. If Parallel Computing Toolbox is not installed, then computation uses parforloops in serial mode. Default is false, which uses forloops in serial mode.  
SquareFormValue  Controls the conversion of the output into a square matrix. Choices are true or false (default).  
AlphabetValue  String specifying the type of sequence (nucleotide or amino acid). Choices are 'NT' or 'AA' (default).  
ScoringMatrixValue  Either of the following:
 
ScaleValue  Positive value that specifies the scale factor used to return the score in arbitrary units. If the scoring matrix information also provides a scale factor, then both are used.  
GapOpenValue  Positive integer that specifies the penalty for opening a gap in the alignment. Default is 8.  
ExtendedGapValue  Positive integer that specifies the penalty for extending a gap. Default is equal to GapOpenValue. 
D  Vector that contains biological distances between each pair of sequences stored in the M elements of Seqs. 
D = seqpdist(Seqs) returns D, a vector containing biological distances between each pair of sequences stored in the M sequences of Seqs, a cell array of sequences, a vector of structures, or a matrix or sequences.
D is a 1by(M*(M1)/2) row vector corresponding to the M*(M1)/2 pairs of sequences in Seqs. The output D is arranged in the order ((2,1),(3,1),..., (M,1),(3,2),...(M,2),...(M,M1)). This is the lowerleft triangle of the full MbyM distance matrix. To get the distance between the Ith and the Jth sequences for I > J, use the formula D((J1)*(MJ/2)+IJ).
D = seqpdist(Seqs,
...'PropertyName', PropertyValue,
...) calls seqpdist with optional properties
that use property name/property value pairs. Specify one or more properties
in any order. Enclose each PropertyName in
single quotation marks. Each PropertyName is
case insensitive. These property name/property value pairs are as
follows:
D = seqpdist(Seqs,
...'Method', MethodValue, ...) specifies
a method to compute distances between each sequence pair. Choices
are shown in the following tables.
Methods for Nucleotides and Amino Acids
Method  Description 

pdistance  Proportion of sites at which the two sequences are different. p is
close to 1 for poorly related sequences, and p is
close to 0 for similar sequences.d = p 
JukesCantor (default)  Maximum likelihood estimate of the number of substitutions between two sequences. p is described with the method pdistance. For nucleotides: d = 3/4 log(1p * 4/3) For amino acids: d = 19/20 log(1p * 20/19) 
alignmentscore  Distance (d) between two sequences (1,
2) is computed from the pairwise alignment score between
the two sequences (score12), and the pairwise alignment
score between each sequence and itself (score11, score22)
as follows:d = (1score12/score11)* (1score12/score22)This option does not imply that prealigned input sequences will be realigned, it only scores them. Use with care; this distance method does not comply with the ultrametric condition. In the rare case where the score between sequences is greater than the score when aligning a sequence with itself, then d = 0 
Methods with No Scoring of Gaps (Nucleotides Only)
Method  Description 

TajimaNei  Maximum likelihood estimate considering the background nucleotide frequencies. It can be computed from the input sequences or given by setting OptArgs to [gA gC gG gT]. gA, gC, gG, gT are scalar values for the nucleotide frequencies. 
Kimura  Considers separately the transitional nucleotide substitution and the transversional nucleotide substitution. 
Tamura  Considers separately the transitional nucleotide substitution, the transversional nucleotide substitution, and the GC content. GC content can be computed from the input sequences or given by setting OptArgs to the proportion of GC content (scalar value from 0 to 1). 
Hasegawa  Considers separately the transitional nucleotide substitution, the transversional nucleotide substitution, and the background nucleotide frequencies. Background frequencies can be computed from the input sequences or given by setting the OptArgs property to [gA gC gG gT]. 
NeiTamura  Considers separately the transitional nucleotide substitution between purines, the transitional nucleotide substitution between pyrimidines, the transversional nucleotide substitution, and the background nucleotide frequencies. Background frequencies can be computed from the input sequences or given by setting the OptArgs property to [gA gC gG gT]. 
Methods with No Scoring of Gaps (Amino Acids Only)
Method  Description 

Poisson  Assumes that the number of amino acid substitutions at each site has a Poisson distribution. 
Gamma  Assumes that the number of amino acid substitutions at each site has a Gamma distribution with parameter a. Set a using the OptArgs property. Default is 2. 
You can also specify a userdefined distance function using @, for example, @distfun. The distance function must have the form:
function D = distfun(S1, S2, OptArgsValue)
The distfun function takes the following arguments:
S1 , S2 — Two sequences of the same length (nucleotide or amino acid).
OptArgsValue — Optional problemdependent arguments.
The distfun function returns a scalar that represents the distance between S1 and S2.
D = seqpdist(Seqs, ...'Indels', IndelsValue, ...) specifies how to treat sites with gaps. Choices are:
score (default) — Scores these sites either as a point mutation or with the alignment parameters, depending on the method selected.
pairwisedel — For every pairwise comparison, it ignores the sites with gaps.
completedel — Ignores all the columns in the multiple alignment that contain a gap. This option is available only if you provided a multiple alignment as the input Seqs.
D = seqpdist(Seqs, ...'OptArgs', OptArgsValue, ...) passes one or more arguments required or accepted by the distance method specified by the Method property. Use a string or cell array to pass one or more input arguments. For example, provide the nucleotide frequencies for the TajimaNei distance method, instead of computing them from the input sequences.
D = seqpdist(Seqs, ...'PairwiseAlignment', PairwiseAlignmentValue, ...) controls the global pairwise alignment of input sequences (using the nwalign function), while ignoring the multiple alignment of the input sequences (if any). Default is:
true — When all input sequences do not have the same length.
false — When all input sequences have the same length.
Tip If your input sequences have the same length, seqpdist assumes they are aligned. If they are not aligned, do one of the following:

D = seqpdist(Seqs, ...'UseParallel', UseParallelValue, ...) specifies whether to use parforloops when calculating the pairwise distances. When true, and Parallel Computing Toolbox is installed and a parpool is open, computation occurs in parallel. If there are no open parpool, but automatic creation is enabled in the Parallel Preferences, the default pool will be automatically open and computation occurs in parallel. If Parallel Computing Toolbox is installed, but there are no open parpool and automatic creation is disabled, then computation uses parforloops in serial mode. If Parallel Computing Toolbox is not installed, then computation uses parforloops in serial mode. Default is false, which uses forloops in serial mode.
D = seqpdist(Seqs, ...'SquareForm', SquareFormValue ...) controls the conversion of the output into a square matrix such that D(I,J) denotes the distance between the Ith and Jth sequences. The square matrix is symmetric and has a zero diagonal. Choices are true or false (default). Setting Squareform to true is the same as using the squareform function in Statistics Toolbox™ .
D = seqpdist(Seqs, ...'Alphabet', AlphabetValue, ...) specifies the type of sequence (nucleotide or amino acid). Choices are 'NT' or 'AA' (default).
The remaining input properties are available when the Method property equals 'alignmentscore' or the PairwiseAlignment property equals true.
D = seqpdist(Seqs, ...'ScoringMatrix', ScoringMatrixValue, ...) specifies the scoring matrix to use for the global pairwise alignment. Default is:
'NUC44' — When AlphabetValue equals 'NT'.
'BLOSUM50' — When AlphabetValue equals 'AA'.
D = seqpdist(Seqs, ...'Scale', ScaleValue, ...) specifies the scale factor used to return the score in arbitrary units. Choices are any positive value. If the scoring matrix information also provides a scale factor, then both are used.
D = seqpdist(Seqs, ...'GapOpen', GapOpenValue, ...) specifies the penalty for opening a gap in the alignment. Choices are any positive integer. Default is 8.
D = seqpdist(Seqs, ...'ExtendGap', ExtendGapValue, ...) specifies the penalty for extending a gap in the alignment. Choices are any positive integer. Default is equal to GapOpenValue.
Read amino acid alignment data into a MATLAB structure.
seqs = fastaread('pf00002.fa');
For every possible pair of sequences in the multiple alignment, ignore sites with gaps and score with the scoring matrix PAM250.
dist = seqpdist(seqs,'Method','alignmentscore',... 'Indels','pairwisedelete',... 'ScoringMatrix','pam250');
Force the realignment of each sequence pair ignoring the provided multiple alignment.
dist = seqpdist(seqs,'Method','alignmentscore',... 'Indels','pairwisedelete',... 'ScoringMatrix','pam250',... 'PairwiseAlignment',true);
Measure the JukesCantor pairwise distances after realigning each sequence pair, counting the gaps as point mutations.
dist = seqpdist(seqs,'Method','jukescantor',... 'Indels','score',... 'Scoringmatrix','pam250',... 'PairwiseAlignment',true);
dnds  dndsml  fastaread  multialign  nwalign  pdist  phytree  seqlinkage