Provided predicates

Predefined predicates are shown in table 1.1.

  

Table: Provided predicates
Table: Provided predicates (continued)

Module	Predicate	Description
Module	Predicate	Description
nj	nj/4	Reconstruction of trees by the neighbor joining method from a given sequence set
traverse	traverse/4	Optimization of branch lengths in terms of the maximum likelihood (for amino acids)
traverse	convert_tree/2	Conversion of branch lengths in a tree from substitutions per site to a probability (for amino acids)
traverse	a_i/6	Computation of $A_i = \sum_{s=1}^n \pi_s L_s^{(i)} L_s^{(j)}$ (for amino acids)
traverse	b_i/6	Computation of $B_i = \sum_{s_i=1}^n \pi_{s_i} L_{s_i}^{(i)} \sum_{s_j=1}^n \pi_{s_j} L_{s_j}^{(j)}$ (for amino acids)
traverse	clike/8	Computation of conditional likelihood (for amino acids)
traverse	state_probability/2	Obtaining $\pi_s$ (for amino acids)
traversen	traversen/4	Optimization of branch lengths in terms of the maximum likelihood (for nucleotides)
traversen	convert_tree/2	Conversion of branch lengths from substitutions per site to a probability (for nucleotides)
traversen	a_i/6	Computation of $A_i = \sum_{s=1}^n \pi_s L_s^{(i)} L_s^{(j)}$ (for nucleotides)
traversen	b_i/6	Computation of $B_i = \sum_{s_i=1}^n \pi_{s_i} L_{s_i}^{(i)} \sum_{s_j=1}^n \pi_{s_j} L_{s_j}^{(j)}$ (for nucleotides)
traversen	clike_8	Computation of conditional likelihood (for nucleotides)
traversen	state_probability/2	Obtaining $\pi_s$ (for nucleotides)
ancestor	ancestor/3	Inference an ancestral sequence of amino acids
ancestorn	ancestor/3	Inference an ancestral sequence of nucleotides
dismat	get_elements/3	Retrieval of elements of a matrix
dismat	get_element/3	Retrieval of an element of a matrix
format	format/3	Format of given sequences to suit traverse/3 and traversen/3
format	count_sites/2	Counting number of sites in a given sequence
format	write/2	Making input file for program test_tra
list	join/3	Concatenation of a pair of lists
list	join_lists/2	Concatenation of arbitrary number of lists
list	get_flat_list/2	Making ``flat'' list from a nested list
list	select_three/2	Extraction of all possible three elements from a list
list	count_letters/3	Computation of frequencies of letters in a given string, which must be a list of letters
list	merge/2	Merging two data streams
list	list_subtract/3	Subtraction of two given lists
list	member/3	Does an element belong to a list?
list	list_size/2	Getting size of a list
list	nonredundant/2	Getting the nonredundant list from a list
list	remove_element/3	Removal of a element from a list
list	qsort/2	Quick sort
list	qsorts/2	Quick sort with the first element of a list as a query
list	add_sort/3	Sorting huge number of entries with the first element as key, and returning top x entries ( $1 \leq x \leq n$, where n is number of elements)
list	add_sort_atom/3	Sorting huge number of entries, and returning top x entries ( $1 \leq x \leq n$, where n is number of elements)
list	nonredundant_plus/2	Getting the nonredundant list from a list with frequencies of redundant elements. The key must be an integer
list	n/2	Count of number of elements in a list
ml	ml/4	Exhaustive search of a tree using the maximum likelihood method (only for nucleotides).
otermio	read_terms/2	Input of prolog-like terms
otermio	putt/1	Output of a prolog-like term
otermio	putts/1	Output of a prolog-like terms
otermio	plot_xyz/1	Output of xyz-axes data for a 3D graph using gnuplot
otermio	plot_3d/1	Output of z-axis data for a 3D graph using gnuplot
pml	pml/10	The maximum likelihood estimation of branch lenghts of a tree under a certain model with amino acid sequences (Source cords of protml [Adachi and Hasegawa, 1996] were used)
sim	sim/5	Simulation of evolution using a model tree (for amino acids)
simn	sim/5	Simulation of evolution using a realized model tree (for nucleotides)
simn_poisson	sim/5	Simulation of evolution using a expected model tree under the Poisson process (for nucleotides)
string	str2int/2	Conversion from a string to an integer
string	str2lst/2	Conversion from a string to a list
string	search_str/3	Search in a string with a string query
string	split/3	Splitting a string into two substrings
string	replace/4	Replacing the first string which matches a query by another string
string	replace/5	Replacing the first string which matches a query by another string, and returning a remained string after the string appear
seq	get_seq/5	Reading an interleaved aligned sequence file
list	invert/2	Naive inversion of a list
string	join_strs/2	Joining arbitrary number of strings
tree	connect/4	Finding children for a given root and a branch in an unrooted tree
tree	connect/3	Finding children for a given root in a tree
tree	topology/2	Generation of all possible topologies for given number of sequences
tree	c2b/2	Conversion of trees from ``cluster format'' to ``branch format''.
tree	convert_c2b	Conversion of a tree from ``cluster format'' to ``branch format''.
tree	get_length	Getting a length of a given branch (parent-child pair)
tree	make_tree/3	Making a tree of functor from ``branch format'' tree
seq2	get_headers/2	Getting headers of multiple aligned sequence file by ClustalW
seq2	get_seqs/2	Getting sequences of multiple aligned sequence file by ClustalW
seq2	read_lines/2	Reading a file line by line
tree	convert_tree	Conversion from a rooted tree format (functor format) to an unrooted format (``branch'' format)
tree	b2c/3	Conversion from ``branch format'' to ``cluster'' format
tree	tdistance	Computation of topological distance between two topologies
tree	tree2b/2	Conversion from a tree to ``branch format''
tree	parent/3
probability	factorial/2	Computation of factorial for a floating point number
probability	b/4	Computation of a term of binomial distribution
probability	c/3	Computation of number of combinations nCr
probability	p/3	Computation of number of permutations nPr
probability	poisson/3	Computation of a term of Poisson distribution