
file  compo_heap.h [code] 
 Declares a "heap" data structure that is used to store computed alignments when composition adjustment of scoring matrices is used.


file  compo_mode_condition.h [code] 
 Declarations of functions used to choose the mode for compositionbased statistics.


file  composition_adjustment.h [code] 
 Definitions used in compositional score matrix adjustment.


file  composition_constants.h [code] 
 Constants used in compositional score matrix adjustment.


file  matrix_frequency_data.h [code] 
 Definitions used to get joint probabilities for a scoring matrix.


file  nlm_linear_algebra.h [code] 
 Declarations for several linear algebra routines.


file  optimize_target_freq.h [code] 
 Routines for finding an optimal set of target frequencies for the purpose of generating a compositionally adjusted score matrix.


file  redo_alignment.h [code] 
 Definitions used to redo a set of alignments, using either composition matrix adjustment or the SmithWaterman algorithm (or both.)


file  smith_waterman.h [code] 
 Definitions for computing SmithWaterman alignments.


file  unified_pvalues.h [code] 
 Headers for computing a "composition" pvalue of a match, and for computing a unified pvalue combining the customary alignment pvalue and the new composition pvalue.

