Clustal Omega  1.0.3
Functions
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.

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_pCreated upgma tree. will be allocated here. use FreeMuscleTree() to free
[in]prMSeqMultiple sequences
[in]iPairDistTypeDistance measure for pairwise alignments
[in]pcGuidetreeOutPassed down to GuideTreeUpgma()
Returns:
Zero on success, non-zero on error