DCJ-indel and DCJ-substitution distances with distinct operation costs

da Silva, Poly H; Machado, Raphael; Dantas, Simone; Braga, Marília DV

doi:10.1186/1748-7188-8-21

Algorithms for Molecular Biology

Table 2 All recombination groups that determine the deductions for computing the DCJ-indel distance

From: DCJ-indel and DCJ-substitution distances with distinct operation costs

	Sources	Resultants	DCJ seq.	Δ _{D C J-λ}	skip if
$P$	$A A_{A B} + B B_{A B}$	2 ∙	o _-2	−2w
$Q$	$2 A A_{A B} + B B_{A} + B B_{B}$	4 ∙	2o_-1≺n_-2	1−4w	$w \leq \frac{1}{2}$
	$2 B B_{A B} + A A_{A} + A A_{B}$	4 ∙		1−4w
$T$	$A A_{A B} + B B_{A} + A B_{A B}$	3 ∙	o_-1≺n_-2	1−3w	$w \leq \frac{1}{2}$
	$A A_{A B} + B B_{B} + A B_{B A}$	3 ∙		1−3w
	$B B_{A B} + A A_{A} + A B_{B A}$	3 ∙		1−3w
	$B B_{A B} + A A_{B} + A B_{A B}$	3 ∙		1−3w
	$2 B B_{A B} + A A_{A}$	$2 ∙ + B B_{B}$		1−3w
	$2 B B_{A B} + A A_{B}$	$2 ∙ + B B_{A}$		1−3w
	$2 A A_{A B} + B B_{A}$	$2 ∙ + A A_{B}$		1−3w
	$2 A A_{A B} + B B_{B}$	$2 ∙ + A A_{A}$		1−3w
$S_{1}$	$A A_{A} + B B_{A}$	2 ∙	o _-1	−w
	$A A_{B} + B B_{B}$	2 ∙		−w
	$A A_{A B} + B B_{A}$	$∙ + A B_{B A}$		−w
	$A A_{A B} + B B_{B}$	$∙ + A B_{A B}$		−w
	$B B_{A B} + A A_{A}$	$∙ + A B_{A B}$		−w
	$B B_{A B} + A A_{B}$	$∙ + A B_{B A}$		−w
$S_{2}$	$A B_{A B} + A B_{B A}$	2 ∙	n _-2	1−2w	$w \leq \frac{1}{2}$
	$A A_{A B} + A B_{A B}$	$∙ + A A_{A}$		1−2w
	$A A_{A B} + A B_{B A}$	$∙ + A A_{B}$		1−2w
	$B B_{A B} + A B_{A B}$	$∙ + B B_{B}$		1−2w
	$B B_{A B} + A B_{B A}$	$∙ + B B_{A}$		1−2w
	$A A_{A B} + A A_{A B}$	$A A_{A} + A A_{B}$		1−2w
	$B B_{A B} + B B_{A B}$	$B B_{A} + B B_{B}$		1−2w
$M$	$2 A B_{A B} + A A_{B} + B B_{A}$	4 ∙	2n_-1≺o_-2	2−4w	$w \leq \frac{1}{2}$
	$2 A B_{B A} + A A_{A} + B B_{B}$	4 ∙		2−4w
$N_{1}$	$A B_{A B} + A A_{B} + B B_{A}$	$2 ∙ + A B_{B A}$	n_-1≺o_-1	1−2w	$w \leq \frac{1}{2}$
	$A B_{B A} + A A_{A} + B B_{B}$	$2 ∙ + A B_{A B}$		1−2w
$N_{2}$	$2 A B_{A B} + A A_{B}$	$2 ∙ + A A_{A}$	n_-1≺n_-2	2−3w	$w \leq \frac{2}{3}$
	$2 A B_{A B} + B B_{A}$	$2 ∙ + B B_{B}$		2−3w
	$2 A B_{B A} + A A_{A}$	$2 ∙ + A A_{B}$		2−3w
	$2 A B_{B A} + B B_{B}$	$2 ∙ + B B_{A}$		2−3w

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ISSN: 1748-7188

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