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Tutorial Note 10 Midterm Solutions & Phylogenetic Tree
Tutorial Note 10 Midterm Solutions & Phylogenetic Tree
s
A A G A T Ø
r
Optimal alignment score: 0
C 0 0 -1 -1 -3 -5
Optimal alignments:
A 1 1 0 0 -2 -4
r CA_ACT
A
s AAGA_T
-1 0 0 1 -1 -3
C -3 -2 -1 0 0 -2 r CAAC_T
s _AAGAT
T -3 -2 -1 0 1 -1
r CAA_CT
Ø -5 -4 -3 -2 -1 0 s _AAGAT
• s = GAGTAG$
• From https://www.ncbi.nlm.nih.gov/books/NBK2590/
• ((((Chimp_Vellerosus:0,
Chimp_Schweinfurthii:0):0.04,
Chimp_Troglodytes:0.04):0.09,
European_Human:0.09):0.13, Chimp_Verus:0.13);
CSCI3220 Algorithms for Bioinformatics Tutorial Notes | Fall 2018 28
Maximum Parsimony
• Sequence-based reconstruction method
• Beliefs:
– Mutations are rare
– The simplest explanation is likely the correct one
G[CT]
Upward Phase
[AG]C
AC GC GT AC GC GT
Downward Phase
GC GT
GC GC
AC GC GT AC GC GT
[AGT]CC
TCC
[AG]C[CT] [CT]C[CT]
Number of mutations: 5
Number of possible sets: 4
CSCI3220 Algorithms for Bioinformatics Tutorial Notes | Fall 2018 34
A Summary on Parsimony
Large Parsimony Small Parsimony
Number of mutations Minimum in all cases Minimum subjected to the given tree
topology
No polynomial time
Algorithms Simple version, Extended version
algorithm