header
dnapars: an open-source bioinformatics program

Tag:
Edit edit   Starstar

Program Information

Name: dnapars: an open-source bioinformatics program
Domain: Bioinformatics
Functionality: Infer evolutionary relationships among taxa using aligned sequences of characters, typically DNA or amino acids.
Input: A $u\times v$ matrix, which presents the DNA sequences with $u$ taxa and $v$ nucleotides.The inputs for source and follow-up test cases are represented by $X$ and $X'$ , respectively.
Output: Phylogenetic tree based on the input DNA sequences. The evolutionary steps for the constructed tree, termed as total length. $T$ and $T'$ denote the output trees of $X$ and $X'$,respectively. The total lengths of $T$ and $T'$ are $t$ and $t'$,respectively. 

Reference

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

MR Information

MR1------

Description:
Property: $X'$ is constructed by inserting a number of uninformative sites into $X$ $\Rightarrow$ $T=T'$ and $t=t'$
Source input: $X$
Source output: $T,t$
Follow-up input: $X'$
Follow-up output: $T',t'$
Input relation:
Output relation: $T=T'$ and $t=t'$
Pattern:

MR2------

Description:
Property: $X'$ is constructed by changing every alphabet in every sequence of $X$ according to the same transformation scheme $\Rightarrow$ $T=T'$ and $t=t'$ 
Source input: $X$ 
Source output: $T,t$ 
Follow-up input: $X'$ 
Follow-up output: $T',t'$ 
Input relation:
Output relation: $T=T'$ and $t=t'$
Pattern:

MR3------

Description:
Property: $X'$ is constructed by swapping two sites in $X$ $\Rightarrow$ $T=T'$ and $t=t'$ 
Source input: $X$ 
Source output: $T,t$ 
Follow-up input: $X'$ 
Follow-up output: $T',t'$ 
Input relation:
Output relation: $T=T'$ and $t=t'$
Pattern:

MR4------

Description:
Property: $X'$ is constructed by removing some uninformative sites from $X$ $\Rightarrow$ $T=T'$ and $t=t'$ 
Source input: $X$ 
Source output: $T,t$ 
Follow-up input: $X'$ 
Follow-up output: $T',t'$ 
Input relation:
Output relation: $T=T'$ and $t=t'$
Pattern:

MR5------

Description:
Property: $X'$ is constructed by inserting a number of hypervariable sites into $X$ $\Rightarrow$ $T=T'$  
Source input: $X$ 
Source output: $T,t$ 
Follow-up input: $X'$ 
Follow-up output: $T',t'$ 
Input relation:
Output relation: $T=T'$
Pattern:

MR6------

Description:
Property: $X'$ is constructed by concatenating each sequence with itself $\Rightarrow$ $T=T'$ and $2t=t'$ 
Source input: $X$ 
Source output: $T,t$ 
Follow-up input: $X'$ 
Follow-up output: $T',t'$ 
Input relation:
Output relation: $T=T'$ and $2t=t'$
Pattern:

MR7------

Description:
Property: $X'$ is constructed by adding a duplicate sequence into $X$ $\Rightarrow$ $T$ and $T'$ only differ in the subtree of the duplicate taxon having the same DNA sequence and $t=t'$ 
Source input: $X$ 
Source output: $T,t$ 
Follow-up input: $X'$ 
Follow-up output: $T',t'$ 
Input relation:
Output relation: $T$ and $T'$ only differ in the subtree of the duplicate taxon having the same DNA sequence and $t=t'$
Pattern:

MR8------ $MR_{12}$

Description:
Property: $X'$ is constructed by inserting a number of uninformative sites into $X$ and then changing every alphabet in every sequence according to the same transformation scheme $\Rightarrow$ $T=T'$ and $t=t'$
Source input: $X$
Source output: $T,t$
Follow-up input: $X'$
Follow-up output: $T',t'$
Input relation:
Output relation: $T=T'$ and $t=t'$
Pattern:

MR9------ $MR_{63}$ 

Description:
Property: $X'$ is constructed by concatenating each sequence with itself and then swapping two sites in $X$ $\Rightarrow$ $T=T'$ and $2t=t'$ 
Source input: $X$ 
Source output: $T,t$ 
Follow-up input: $X'$ 
Follow-up output: $T',t'$ 
Input relation:  
Output relation: $T=T'$ and $2t=t'$ 
Pattern:

MR10------ $MR_{24}$ 

Description:
Property: $X'$ is constructed by changing every alphabet in every sequence according to the same transformation scheme and removing some uninformative sites from $X$ $\Rightarrow$ $T=T'$ and $t=t'$ 
Source input: $X$ 
Source output: $T,t$ 
Follow-up input: $X'$ 
Follow-up output: $T',t'$ 
Input relation:  
Output relation: $T=T'$ and $t=t'$ 
Pattern:

MR11------ $MR_{75}$ 

Description:
Property: $X'$ is constructed by adding a duplicate sequence into $X$ and then inserting a number of hypervariable sites into $X$ $\Rightarrow$ $T$ and $T'$ only differ in the subtree of the duplicate taxon having the same DNA sequence 
Source input: $X$ 
Source output: $T,t$ 
Follow-up input: $X'$ 
Follow-up output: $T',t'$ 
Input relation:  
Output relation: $T$ and $T'$ only differ in the subtree of the duplicate taxon having the same DNA sequence 
Pattern:

MR12------ $MR_{15}$ 

Description:
Property: $X'$ is constructed by inserting a number of uninformative sites as well as a number of hypervariable sites into $X$ $\Rightarrow$ $T=T'$ 
Source input: $X$ 
Source output: $T,t$ 
Follow-up input: $X'$ 
Follow-up output: $T',t'$ 
Input relation:  
Output relation: $T=T'$ 
Pattern:
Insert title here