dnapars: an open-source bioinformatics program

### 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