composition_adjustment Directory Reference

Directory dependency graph for composition_adjustment:

Files
file	compo_heap.c [code]
	Defines a "heap" data structure that is used to store computed alignments when composition adjustment of scoring matrices is used.
file	compo_mode_condition.c [code]
	Functions to test whether conditional score matrix adjustment should be applied for a pair of matching sequences.
file	composition_adjustment.c [code]
	Highest level functions to solve the optimization problem for compositional score matrix adjustment.
file	matrix_frequency_data.c [code]
	Joint probabilities for specific matrices.
file	nlm_linear_algebra.c [code]
	Basic matrix and vector operations.
file	optimize_target_freq.c [code]
	Routines for finding an optimal set of target frequencies for the purpose of generating a compositionally adjusted score matrix.
file	redo_alignment.c [code]
	Routines for redoing a set of alignments, using either composition matrix adjustment or the Smith-Waterman algorithm (or both.)
file	smith_waterman.c [code]
	Routines for computing rigorous, Smith-Waterman alignments.
file	unified_pvalues.c [code]
	Procedures for computing a "composition" p-value of a match, and for computing a unified p-value combining the customary alignment p-value and the new composition p-value.