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).
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
- clike/8
- computes a conditional likelihood value (traverse).
Conditional likelihood is defined by
where
is the likelihood of node k with state
.
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
.
- cofactor3/3
- calculates a cofactor (signed minor) for a given 3x3 matrix
(matrix).
:- cofactor3(Matrix M, i, j, Cofactor of the matrix
).
- 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.
Figure 4: A log likelihood surface.
- dX/3
- computes a unbiased
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
(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.
Figure 5: Optimization of branch lengths.