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dnapars

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Program Information

Name: dnapars
Domain: Bioinformatics
Functionality: Inferring evolutionary relationships among taxa using aligned sequences of characters, typically DNA or amino acids.
Input: X:A $u \times v$ matrix(Type:Matrix)
Output: T:The output trees of X(Type:Tree) t:The total length of T(Type:Integer)

Reference


A New Method for Constructing Metamorphic Relations
http://dx.doi.org/10.1109/QSIC.2012.10
 


MR Information

MR1------

Description:
Property:
Source input: $X_s$
Source output: $T_s,t_s$
Follow-up input: $X_f$
Follow-up output: $T_f,t_f$
Input relation: $X_f$ is constructed by inserting a number of uninformative sites into $X_s$.
Output relation: $T_f=T_s$ $t_f=t_s$
Pattern:

MR2------

Description:
Property:
Source input: $X_s$
Source output: $T_s,t_s$
Follow-up input: $X_f$
Follow-up output: $T_f,t_f$
Input relation: $X_f$ is constructed by changing every alphabet in every sequence of $X_s$ according to the same transformation scheme.
Output relation: $T_f=T_s$ $t_f=t_s$
Pattern:

MR3------

Description:
Property:
Source input: $X_s$
Source output: $T_s,t_s$
Follow-up input: $X_f$
Follow-up output: $T_f,t_f$
Input relation: $X_f$ is constructed by swapping two sites in $X_s$.
Output relation: $T_f=T_s$ $t_f=t_s$
Pattern:

MR4------

Description:
Property:
Source input: $X_s$
Source output: $T_s,t_s$
Follow-up input: $X_f$
Follow-up output: $T_f,t_f$
Input relation: $X_f$ is constructed by removing some uninformative sites from $X_s$.
Output relation: $T_f=T_s$ $t_f=t_s$
Pattern:

MR5------

Description:
Property:
Source input: $X_s$
Source output: $T_s,t_s$
Follow-up input: $X_f$
Follow-up output: $T_f,t_f$
Input relation: $X_f$ is constructed by inserting a number of hypervariable sites into $X_s$.
Output relation: $T_f=T_s$
Pattern:

MR6------

Description:
Property:
Source input: $X_s$
Source output: $T_s,t_s$
Follow-up input: $X_f$
Follow-up output: $T_f,t_f$
Input relation: $X_f$ is constructed by concatenating each sequence with itself.
Output relation: $T_f=T_s$ $t_f=2t_s$
Pattern:

MR7------

Description:
Property:
Source input: $X_s$
Source output: $T_s,t_s$
Follow-up input: $X_f$
Follow-up output: $T_f,t_f$
Input relation: $X_f$ is constructed by adding a duplicate sequence into $X_s$.
Output relation: $T_f$ and $T_s$ only differ in the subtree of the duplicate taxon having the same DNA sequence. $t_f=t_s$
Pattern:
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