rewrite the seqneighjoin function in matlab -

i have task rewrite seqneighjoin function in matlab adding frequency of sequences. after searching, understand function returns phylogenetic tree object obtained seqences neighbor joinn method wiki http://en.wikipedia.org/wiki/neighbor_joining now, have following 2 questions. (1): data structure of phytree object obtained function? how express it? example, similar linkage function, returns phylogenetic tree, , data structure clear there, i.e., matrix 3 columns, i-th column indicates nodes combined , corresponding distance when combined. time , attention.

(2): based on wiki, how supposed add frequency function seqneighjoin? totally confused.

thanks time , attention. appreciate that.

edit: following code.

function z = seqneighjoin(d_all, freq)     n = size (d_all, 2);    m=(1+sqrt(8*n+1))/2;    z=zeros(m-1,3);    q=zeros(m,m);    str = zeros (m,m);     % initialize distance matrix d    d=ones(m,m);    d(tril(d,-1)==1)=d_all;    d(triu(d,1)==1)=d_all;    d(eye(m,m)==1) = 1:m;  % diagonal entries of matrix d indices of clusters     % initialize matrix str    r=1:m        c=1:m            str(r,c)=freq(r)*freq(c)*d(r,c);            str(c,r)=freq(r)*freq(c);        end    end        % loop through m-1 times create matrix z     k = 1:m-1         % initialize (for first time) or update (for other times)        % matrix q         colsum = sum(d, 1);         rowsum=sum(d,2);        a=size(colsum, 2);        colsumm=colsum(ones(a,1),:);        rowsunm=rowsum(:,ones(1,a));        q=(a-2)*d-colsumm-rowsumm;            % find minimum element in matrix q        u=min(q);        v=min(u);        [i,j]=find(q==v);        r=i(1);        c=j(1);         % combine d(r,r) , d(c,c) new node m+k         z(k,:)=[d(r,r), d(c,c), v];         % calculate distance between new node m+k , other node        % not m+k         d(r,:) = (d(r,:) + d(c,:) - d(r,c) )/2;        d(r,r) = m+k;        d(c,:)=[]; d(:,c)=[];     end 

here, d_all vector representation of distance matrix returned seqpdist function in matlab, , freq vector indicating frequency of sequences.