src/clustal/mbed.h File Reference

#include "muscle_tree.h"
#include "seq.h"

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Functions
int	Mbed (tree_t **tree, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOutfile)
	From scratch reimplementation of mBed: Blackshields et al. (2010); PMID 20470396.

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Function Documentation

int Mbed	(	tree_t **	prMbedTree_p,
		mseq_t *	prMSeq,
		const int	iPairDistType,
		const char *	pcGuidetreeOut
	)

From scratch reimplementation of mBed: Blackshields et al. (2010); PMID 20470396.

Idea is a follows:

• convert sequences into vectors of distances
• cluster the vectors using k-means
• cluster each of the k clusters using upgma (used cached distances from above?)
• join the sub-clusters to create on tree (use UPGMA on k-means medoids)

Parameters:

[out]	prMbedTree_p	Created upgma tree. will be allocated here. use FreeMuscleTree() to free
[in]	prMSeq	Multiple sequences
[in]	iPairDistType	Distance measure for pairwise alignments
[in]	pcGuidetreeOut	Passed down to GuideTreeUpgma()

Note:

: if the number of sequences is smaller than MAX_ALLOWED_SEQ_PER_PRECLUSTER then there's no need to do the subclustering first. In fact it costs some extra time. However, it's insignificant and for simplicities sake we don't do any special checks

Returns:

Zero on success, non-zero on error