Predefined predicates are shown in table 1.1.
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
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traverse | b_i/6 | Computation of
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traverse | clike/8 | Computation of conditional likelihood (for amino acids) |
traverse | state_probability/2 | Obtaining ![]() |
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
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traversen | b_i/6 | Computation of
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traversen | clike_8 | Computation of conditional likelihood (for nucleotides) |
traversen | state_probability/2 | Obtaining ![]() |
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 (
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list | add_sort_atom/3 | Sorting huge number of entries,
and returning top
x entries (
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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 |