Developer Guide

This guide gives developers an overview of IQ-TREE software, data structure and discusses possibility of implementing new models into IQ-TREE code.

To achieve both high performance and flexibility, IQ-TREE software has been entirely written in object oriented C++. Thus, it faciliates extending with new sequence data types or new models. IQ-TREE code consists of C++ classes, most of which inherits from three basal classes: Alignment, ModelSubst and PhyloTree to handle sequence alignments, models of substitution and phylogenetic trees, respectively. In the following we introduce these basal classes.

TIP: IQ-TREE extensively uses Standard Template Library (STL) in C++. Thus, be first familiar with STL and fundamental STL data structures like string, vector, set and map.

Alignment

The Alignment class stores the data as a vector of Pattern. Each Pattern is in turn a string representing the characters across the sequences at an alignment site, with a frequency of occurrences in the Alignment (from header file pattern.h):

/**
	Site-patterns in a multiple sequence alignment
*/
class Pattern : public string {
public:
	/** 
		constructor
	*/
    Pattern();

    ...
    
	/** 
		destructor
	*/
    virtual ~Pattern();

	/**
		frequency appearance of the pattern
	*/
	int frequency;
};

The rationale for storing the data this way (instead of storing a set of sequences) is that most computations are carried out along the site-patterns of the Alignment. Thus, it makes all operations more convenient and faster.

As noted above, the Alignment class is defined as (from header file alignment.h):

/**
    Multiple Sequence Alignment. Stored by a vector of site-patterns
*/
class Alignment : public vector<Pattern> {
public:
    /**
            constructor
            @param filename file name
            @param sequence_type type of the sequence, either "BIN", "DNA", "AA", or NULL
            @param intype (OUT) input format of the file
     */
    Alignment(char *filename, char *sequence_type, InputType &intype);

    /**
            destructor
     */
    virtual ~Alignment();

    ...

};

NOTICE: Please follow the commenting style of the code when declaring new components (classes, functions or variables). The comments should start with /**, followed by a concise description of the new component, and ended with */. If component is a function, explain the purpose of each parameter with @param keyword, followed by the parameter name and a short description. If the function returns a parameter as output, append (OUT) right after the parameter name. If the function returns a value, add @return followed by a short description of the returned value meaning.