`Name:`

dnapars and dnapenny `Domain:`

Bioinformatics `Functionality:`

Implement the maximum parsimony method to construct Phylogenetic trees `Input:`

An input ﬁle called “inﬁle” consisting of DNA sequences of multiple taxa `Output:`

Trees with the shortest “total length”
Veriﬁcation of Phylogenetic Inference Programs Using Metamorphic Testing 10.1142/S021972001100563X

`Description:`

`Property:`

If we generate a follow-up input X’ by swapping two sites (the columns) in the original input X , then the set of original and follow-up output trees T and T’ are identical and their corresponding total lengths t and t0 are equal `Source input:`

`Source output:`

`Follow-up input:`

`Follow-up output:`

`Input relation:`

`Output relation:`

`Pattern:`

`Description:`

`Property:`

If we add k (k>0) number of uninformative sites into the original input X to generate a follow-up input X’, then the set of original and follow-up output trees T and T’ are identical and their corresponding total lengths t and t’ are equal. Additions of uninformative sites are order independent and can be placed after any site of the original input X `Source input:`

`Source output:`

`Follow-up input:`

`Follow-up output:`

`Input relation:`

`Output relation:`

`Pattern:`

`Description:`

`Property:`

If we remove some uninformative sites from the original input X to generate a follow-up input X’, then the set of original and follow-up output trees T and T’ are identical and their corresponding total lengths t and t’ are equal `Source input:`

`Source output:`

`Follow-up input:`

`Follow-up output:`

`Input relation:`

`Output relation:`

`Pattern:`

`Description:`

`Property:`

If we double the length of DNA sequences in the original input X by the concatenation of each DNA sequence with itself to generate follow-up input X’, then the set of original and follow-up trees T and T’ are identical and the follow- up total length t’ is double of the original total length t. This MR is only true for input alignment with n = 4z where z is a integer number `Source input:`

`Source output:`

`Follow-up input:`

`Follow-up output:`

`Input relation:`

`Output relation:`

`Pattern:`

`Description:`

`Property:`

If we add some hypervariable sites into the original test input X to generate a follow-up input X’, then the set of original and follow-up output trees T and T’ are identical. Hypersensitive site(s) can be placed after any site of the original input X `Source input:`

`Source output:`

`Follow-up input:`

`Follow-up output:`

`Input relation:`

`Output relation:`

`Pattern:`

`Description:`

`Property:`

If we apply the same transformation to change every character in every DNA sequence, for example (A→T, T→G, G→C, C→A), in the original input X to generate follow-up input X’, then the set of original and follow-up trees T and T’ are identical and their corresponding total lengths t and t’ are equal `Source input:`

`Source output:`

`Follow-up input:`

`Follow-up output:`

`Input relation:`

`Output relation:`

`Pattern:`

`Description:`

`Property:`

If we add a duplicate DNA sequences of any taxon in the original input X to create the follow-up input X’. Then- 1. the trees of original and follow-up output sets, T and T’ respectively, should diﬀer only for the duplicate taxa such that in the follow-up output tree, the duplicates are grouped together in a sub tree, and 2. The total lengths of original and follow-up trees t and t’ should be same and the output is independent on where the duplicate DNA sequence is placed `Source input:`

`Source output:`

`Follow-up input:`

`Follow-up output:`

`Input relation:`

`Output relation:`

`Pattern:`