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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


next up previous
Next: Application programs Up: Provided predicates and those Previous: Provided modules
Satoshi OOta
1999-03-06