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 structure like string, vector, set and map.

Alignment

The Alignment class stores the data as a vector of Pattern. Each Pattern is a string representing the characters across the sequences at an alignment site, with a frequency of occurences in the Alignment:

class Pattern : public string
{
public:
	/** 
		constructor
	*/
    Pattern();

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

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