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_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
