- a -

• aligned : mseq_t

- b -

• bAutoOptions : opts_t
• bIterationsAuto : opts_t
• bPrintCR : progress_t
• bUseMbed : opts_t
• bUseMbedForIteration : opts_t

- d -

• data : list_elem_s , symmatrix_t
• destroy : list_t

- f -

• filename : mseq_t

- h -

• head : list_t

- i -

• i1 : two_ints_t
• i2 : two_ints_t
• iClusteringType : opts_t
• iDim : bisecting_kmeans_result_t
• iHMMInputFiles : opts_t
• iLogLevelEnabled : log_t
• iMaxGuidetreeIterations : opts_t
• iMaxHMMIterations : opts_t
• iNClusters : bisecting_kmeans_result_t
• iNumIterations : opts_t
• iPairDistType : opts_t

- k -

• ktup : ktuple_param_t

- m -

• m_bHasEdgeLength1 : tree_t
• m_bHasEdgeLength2 : tree_t
• m_bHasEdgeLength3 : tree_t
• m_bRooted : tree_t
• m_dEdgeLength1 : tree_t
• m_dEdgeLength2 : tree_t
• m_dEdgeLength3 : tree_t
• m_Ids : tree_t
• m_ptrName : tree_t
• m_uCacheCount : tree_t
• m_uNeighbor1 : tree_t
• m_uNeighbor2 : tree_t
• m_uNeighbor3 : tree_t
• m_uNodeCount : tree_t
• m_uRootNodeIndex : tree_t

- n -

• ncols : symmatrix_t
• next : list_elem_s
• nrows : symmatrix_t
• nseqs : mseq_t

- o -

• orig_seq : mseq_t

- p -

• pcDistmatInfile : opts_t
• pcDistmatOutfile : opts_t
• pcGuidetreeInfile : opts_t
• pcGuidetreeOutfile : opts_t
• pcLastLogMsg : progress_t
• pcPrefix : progress_t
• piIndex : sortwithindex_t
• piNObjsPerCluster : bisecting_kmeans_result_t
• piValue : sortwithindex_t
• ppcHMMInput : opts_t
• ppdClusterCenters : bisecting_kmeans_result_t
• ppiObjIndicesPerCluster : bisecting_kmeans_result_t
• prFile : progress_t
• prFP : log_t
• prFunc : log_t
• prPrefix : log_t
• prStopwatch : progress_t

- r -

• rHhalignPara : opts_t

- s -

• seq : mseq_t
• seqtype : mseq_t
• signif : ktuple_param_t
• size : list_t
• sqinfo : mseq_t

- t -

• tail : list_t

- w -

• wind_gap : ktuple_param_t
• window : ktuple_param_t