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Computational Phylogenetic - Essay Example

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Keep all program parameters set to default. Copy/Paste the distance matrix as your answer.
Using the corresponding distance matrix generated as your…
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Computational Phylogenetic
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UMUC BIOT630 Lecture 7 Exercise – “Due Version” MOBYLE Portal url = http mobyle.pasteur.fr/cgi-bin/portal.py# Question Using the following MSA:
>Human/1292
MGRQKELVSRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGIL
IAGQVSGAHLNPAVTFAMCFLAREPWIKLPIYTLAQTLGAFLGAGIVFGLYYDAIWHFADNQLFVSGPNGTA
GIFATYPSGHLDMINGFFDQFIGTASLIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNP
ARDFGPRLFTALAGWGSAVFTTGQHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEQ--PPPSNEEENVKLAHV
KHKEQI
>Monkey/1-292
MGRQKELMSRCGEMLHIRHRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGIL
IAGQVSGAHLNPAVTFAMCFLAREPWIKLPVYTLAQTLGAFLGAGIVFGLYYDAIWGFADNQLFVSGPNGTA
GIFATYPSGHLDMINGFFDQFIGTASLIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNP
ARDFGPRLFTALAGWGSKVFTTGRHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEQ--PPPSTEQENVKLAHV
KHKEQI
>Cow/1-292
MGRQKELVNRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGIL
IAGQVSGAHLNPAVTFAMCFLAREPWIKLPVYTLAQTLGAFLGAGIIFGLYYDAIWAFANNQLIVSGPNGTA
GIFATYPSGHLDMVNGFFDQFIGTASLIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNP
ARDFGPRLFTAIAGWGSEVFTTGRHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEP--PPPSTDEENVKLSHV
KHKEQM
>Pig/1-290
MGRQKELVTRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGIL
VAGQVSGAHLNPAVTFAMCFLAREPWIKLPVYTLAQTLGAFLGAGIIFGLYYDAIWAFANNQLIVSGPNGTA
GIFATYPSGHLDMVNGFFDQFIGTASLIVCVLAIVDPNNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNP
ARDFGPRLFTAIAGWGSEVFTTGRHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEP--PPPSTDEENVKLSQV
KHKE--
>Horse/1-292
MGRQKELVSRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGIL
VAGQVSGAHLNPAVTFAMCFLAREPWIKLPIYTLAQTLGAFLGAGIIFGLYYDAIWAFANNQLIVSGPNGTA
GIFATYPSGHLDMVNGFFDQFIGTAALIVCVLAIVDPYNNPVPRGLQAFTVGLVVLVIGTSMGFNSGYAVNP
ARDFGPRLFTAIAGWGSEVFTTGRHWWWVPIISPLLGSIAGVFVYQLMIGCHLEQ--PPPSTEQENVKLAHV
KHKEQI
>Dog/1-292
MGRQKELVSRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGIL
VAGQVSGAHLNPAVTFAMCFLAREPWIKLPVYALAQTLGAFLGAGIVFGLYYDAIWDFAKNELVVSGPNGTA
GIFATYPSGHLDMVNGFFDQFIGTASLIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNP
ARDFGPRLFTAIAGWGSEVFTTGRHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEQ--PPSSTEQENVKLAHV
KHKEQI
>Mouse/1-292
MGRQKELMNRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGIL
VAGQVSGAHLNPAVTFAMCFLAREPWIKLPIYALAQTLGAFLGAGIVFGLYYDAIWAFANNELFVSGPNGTA
GIFATYPSGHLDMVNGFFDQFIGTAALIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNP
ARDFGPRLFTALAGWGSEVFTTGRHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEQ--PPPSTEEENVKLAHM
KHKEQI
>Rat/1-292
MGRQKELMNRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLAIL
VAGQVSGAHLNPAVTFAMCFLAREPWIKLPIYTLAQTLGAFLGAGIVFGLYYDAIWAFAGNELVVSGPNGTA
GIFATYPSGHLDMVNGFFDQFIGTAALIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNP
ARDFGPRLFTALAGWGSEVFTTGQNWWWVPIVSPLLGSIGGVFVYQLMIGCHLEQ--PPPSTEAENVKLAHM
KHKEQI
>Chicken/1-292
MGRQKDVLATIEEHLRIRNKLVRQALAECLGTLILVLFGCGSVAQIVLSRGTHGGFLTVNLAFGFAVMLGIL
IAGQVSGGHLNPAVTFAMCFLAREPWIKLPVYALAQTLGAFLGAGIVFGLYHDAIWAFGSNHLYVTGENATA
GIFATYPSQHLNVVNGFFDQFIGTASLIVCVLAIVDPFNNPVPPGLEAFTVGFVVLVIGTSMGFYSGYAVNP
ARDFGPRLFTAIAGWGTEVFWTGKQWWWVPIVAPFLGAIAGVIVYQLMIGCHDEP--SPPASEQETVKLANV
KHKERV
>Frog/1-294
MGRQKDFINKCNQLLRLRNKLLRQALSECLGTLILVMFGCGSVAQVVLSKGSHGQFLTVNLAFGFAVMLGIL
ISGQVSGGHLNPAVTFALCIMAREPWIKFPIYSFAQTLGAFLGAGIIYGLYYDAIWFFGNDQLFVMGENGTA
GIFTTFPSEHLTLINGFFDQFIGTAALIVCVLAIVDPNNNPIPRGLEAFTVGFVVLVIGTSMGFNSGYAVNP
ARDFGPRLFTSLAGWGTEVFWAGNQWWWVPIVSPLLGAFTGVLVYQLMIGCHIEPAQTPQSTEQENIKLADV
KNKDRI
… generate the corresponding distance matrix using the PROTDIST program found at the MOBYLE Portal under phylogeny/distance. Keep all program parameters set to default. Copy/Paste the distance matrix as your answer.
Answer:
10
Human/1292 0.000000 0.029038 0.054794 0.062786 0.050998 0.051271
0.047527 0.058924 0.226711 0.264448
Monkey/1-2 0.029038 0.000000 0.054409 0.062342 0.050616 0.043780
0.047020 0.062200 0.216003 0.260350
Cow/1-292 0.054794 0.054409 0.000000 0.014360 0.039421 0.050476
0.050841 0.069528 0.212661 0.269528
Pig/1-290 0.062786 0.062342 0.014360 0.000000 0.039782 0.050941
0.055094 0.074030 0.211011 0.267450
Horse/1-29 0.050998 0.050616 0.039421 0.039782 0.000000 0.039464
0.039726 0.054616 0.223549 0.264562
Dog/1-292 0.051271 0.043780 0.050476 0.050941 0.039464 0.000000
0.039882 0.054988 0.210443 0.279946
Mouse/1-29 0.047527 0.047020 0.050841 0.055094 0.039726 0.039882
0.000000 0.028945 0.222880 0.261103
Rat/1-292 0.058924 0.062200 0.069528 0.074030 0.054616 0.054988
0.028945 0.000000 0.239230 0.278508
Chicken/1- 0.226711 0.216003 0.212661 0.211011 0.223549 0.210443
0.222880 0.239230 0.000000 0.266608
Frog/1-294 0.264448 0.260350 0.269528 0.267450 0.264562 0.279946
0.261103 0.278508 0.266608 0.000000
Question 2.
Using the corresponding distance matrix generated as your answer in Question 1, perform UPGMA using the “neighbor” program found at the MOBYLE Portal under phylogeny/distance. Keep all program parameters set to default except for the parameter you will need to change to run “UPGMA” instead of “Neighbor-joining”. Copy/Paste the resulting “neighbor.outtree” as your answer.
Answer:
(((((Human/1292:0.01452,Monkey/1-2:0.01452):0.01242,((Cow/1-292:0.00718,
Pig/1-290:0.00718):0.01540,(Horse/1-29:0.01973,Dog/1-292:0.01973):0.00285):0.00436):0.00033,
(Mouse/1-29:0.01447,Rat/1-292:0.01447):0.01279):0.08289,
Chicken/1-:0.11016):0.02387,Frog/1-294:0.13403);
Question 3.
Using the resulting “neighbor.outtree” generated as your answer in Question 2, generate the corresponding dendrogram using the “drawgram” program found at the MOBYLE Portal under phylogeny/display. Keep all program parameters set to default except for the “Drawgram options” parameter; you will need to change this parameter to a file type you can visualize on your computer (e.g., Windows – BitMap). Copy/Paste the resulting image as your answer.
Answer:
Question 4.
Using the following MSA (copy all lines including the line with the 5 and 13):
5 13
Alpha AACGUGGCCAAAU
Beta AAGGUCGCCAAAC
Gamma CAUUUCGUCACAA
Delta GGUAUUUCGGCCU
Epsilon GGGAUCUCGGCCC
Run the “dnapars” program found at the MOBYLE Portal under phylogeny/parsimony. Keep all program parameters set to default. Copy/Paste the resulting “dnapars.outtree” as your answer.
Answer:
(((Epsilon:0.09615,Delta:0.13462):0.48718,Gamma:0.27564):0.21795,
Beta:0.07692,Alpha:0.17308);
Question 5.
Using the resulting “dnapars.outtree” generated as your answer in Question 4, generate the corresponding dendrogram using the “drawtree” program found at the MOBYLE Portal under phylogeny/display. Keep all program parameters set to default except for the “Drawtree Options” parameter; you will need to change this parameter to a file type you can visualize on your computer (e.g., Windows – BitMap). Copy/Paste the resulting image as your answer.
Answer:
Question 6.
Using the following distance matrix (copy all lines including the line with the 5):
5
Alpha 0.000000 0.330447 0.625670 1.032032 1.354086
Beta 0.330447 0.000000 0.375578 1.096290 0.677616
Gamma 0.625670 0.375578 0.000000 0.975798 0.861634
Delta 1.032032 1.096290 0.975798 0.000000 0.226703
Epsilon 1.354086 0.677616 0.861634 0.226703 0.000000
Run the “fitch” program found at the MOBYLE Portal under phylogeny/distance. Keep all program parameters set to default except for the parameter you will need to change to run “Minimum Evolution” instead of “Fitch-Margoliash”. Copy/Paste the resulting “fitch.outtree” as your answer.
Answer:
(Beta:0.03057,((Epsilon:0.04118,Delta:0.18553):0.58050,Gamma:0.22673):0.11319,Alpha:0.29988);
Question 7.
Using the resulting “fitch.outtree” generated as your answer in Question 6, generate the corresponding dendrogram using the “drawtree” program found at the MOBYLE Portal under phylogeny/display. Keep all program parameters set to default except for the “Drawtree Options” parameter; you will need to change this parameter to a file type you can visualize on your computer (e.g., Windows – BitMap). Copy/Paste the resulting image as your answer.
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