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Description of the provided predicates

Module names appeared in parentheses.

ancestor/6
infers an ancestral site of a pair of descendants (ancestor). See Fig. 2.

:- ancestor(States_1,States_2,V_1,V_2,States_0,Likelihoods).

 

  figure46


Figure 2: ancestor/6.

beautify/2
beautifies a printed format of a nested list structure, especially for expressing structure of a database (beautify).
b/4
generates a binomial distribution (probability).
c/3
takes a binomial coefficient (probability).
c2b/2
converts a cluster-like topology format to a branch-like one (tree).

For example, [[1,2],[3,4],5] will be converted to

displaymath237

clike/8
computes a conditional likelihood value (traverse).

Conditional likelihood is defined by

  equation68

where tex2html_wrap_inline239 is the likelihood of node k with state tex2html_wrap_inline243 . tex2html_wrap_inline239 is the product of likelihoods regarding two children nodes i and j and two transition probabilities between node k and i, j (see Fig. 3).

  
Figure 3: Recursive definition of conditional likelihood tex2html_wrap_inline233 .

cofactor3/3
calculates a cofactor (signed minor) for a given 3x3 matrix (matrix).

:- cofactor3(Matrix M, i, j, Cofactor of the matrix tex2html_wrap_inline307 ).

consensus/2
generates the consensus sequence for a given set of sequences (consensus).

:- consensus(Sequences, The consensus Sequence).

connect/3
finds the descendant nodes for a given node (tree).

:- connect(A tree, A given node, The descendant nodes).

connect/4
finds the descendant nodes for a given node in a unrooted tree (tree).

:- connect(A Tree, A Branch which determines the root of a subtree, A Node, The descendant nodes).

convert_tree/2
converts a distance (number of substitution) to an internal expression P (traverse).

:- convert_tree(A tree presented by distances, The tree presented by internal expression Ps).

curvature/5
draws a likelihood surface for given two nucleotide sequences in a tree (curvature). See Fig. 4.

   figure76
Figure 4: A log likelihood surface.

dX/3
computes a unbiased tex2html_wrap_inline261 for given sequences (dX).
det2/2
calculates a determinant of a given 2x2 matrix (matrix).
det3/2
calculates a determinant of a given 3x3 matrix (matrix).
divide/3
divides a list into a given number of segments equally (divide).
dot_matrix/5
generates a dot matrix (dot_matrix).
extract_author/2
extracts authors from PIR database (extract_author).
extract_fields/3
extracts selected fields from PIR database (extract_fields).
factorial/2
takes an approximate factorial to a given floating point number (float).
factorial/2
takes an exact factorial to a given integer (int).
floatadd/3
adds floating point data having arbitrary accuracy (add).
format/2
makes formatted lists from blocked lines (format).
fx/8
computes tex2html_wrap_inline263 (fx).
get_seq
reads aligned sequences, and makes a character state format (get_seq).
interleave/2
converts an interleaved format to a blocked format (interleave).
invert/2
inverts an order of a given list (invert).
lines2string/2
converts given lines to a string (lines2string).
join/3
joins two lists (list).
join_lists/2
joins lists (list).
get_flat_list/2
gets a flat list from a nested list (list).
log_like/5
computes log likelihood for a given tree (log_like).
make_bib/2
makes a bibliography from PIR database (make_bib).
make_destbl/2
makes a description table for annotating a given tree (make_destbl).
make_gap_matrix/2
makes a minimum gap matrix (MGM) (make_gap_matrix).
make_records/2
makes records from PIR database (make_records).
make_seq/2
extract sequences from PIR database, and converts them to FASTA format (make_seq).
minor3/2
calculates a minor of a given 3x3 matrix (matrix).
minorm/4
generates a minor matrix of a given matrix (matrix).
newton/7
solves a given equation by the newton method (newton).
p/3
calculates number of permutations (probability).
plot_like/3
plots likelihood values (plot_like).
plot_xyz/1
plots 3-D coordinates from a given list(termio).
print_sequences/2
prints sequence from a list of integer-presented sequence data (print_sequences).
putt/1
puts a Prolog term to standard output (termio).
putts/1
puts a Prolog terms to standard output (termio).
read_terms/2
reads Prolog terms from a given file (termio).
remove_gap_site/2
removes gap sites from given sequences, and generates input file for traverse/3 (remove_gap_site).
search_str/3
searches a string (search_str).
starling/2
calculates a factorial by Starling's formula (probability).
str2lst/2
converts a string to a list (string).
synonymous/3
computes numbers of synonymous and nonsynonymous sites of a given sequence (synonymous).
topology/2
generates a topology space for a given number of sequences (tree).
traverse/4
optimizes branch lengths of a given trees according to likelihood values (traverse). See Fig. 5.

   figure96
Figure 5: Optimization of branch lengths.


next up previous
Next: How to make and Up: The application program Previous: Files


Mon Jan 12 07:51:29 JST 1998