Clustal Omega  1.2.4
Functions
mbed.h File Reference
#include "muscle_tree.h"
#include "seq.h"
Include dependency graph for mbed.h:
This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Functions

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

Function Documentation

◆ Mbed()

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

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()
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