Computational Phylogenetic - Essay Example

UMUC BIOT630 Lecture 7 Exercise – “Due Version” MOBYLE Portal url = http mobyle.pasteur.fr/cgi-bin/portal.py# Question Using the following MSA: >Human/1292MGRQKELVSRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGILIAGQVSGAHLNPAVTFAMCFLAREPWIKLPIYTLAQTLGAFLGAGIVFGLYYDAIWHFADNQLFVSGPNGTAGIFATYPSGHLDMINGFFDQFIGTASLIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNPARDFGPRLFTALAGWGSAVFTTGQHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEQ--PPPSNEEENVKLAHVKHKEQI>Monkey/1-292MGRQKELMSRCGEMLHIRHRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGILIAGQVSGAHLNPAVTFAMCFLAREPWIKLPVYTLAQTLGAFLGAGIVFGLYYDAIWGFADNQLFVSGPNGTAGIFATYPSGHLDMINGFFDQFIGTASLIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNPARDFGPRLFTALAGWGSKVFTTGRHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEQ--PPPSTEQENVKLAHVKHKEQI>Cow/1-292MGRQKELVNRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGILIAGQVSGAHLNPAVTFAMCFLAREPWIKLPVYTLAQTLGAFLGAGIIFGLYYDAIWAFANNQLIVSGPNGTAGIFATYPSGHLDMVNGFFDQFIGTASLIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNPARDFGPRLFTAIAGWGSEVFTTGRHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEP--PPPSTDEENVKLSHVKHKEQM>Pig/1-290MGRQKELVTRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPVYTLAQTLGAFLGAGIIFGLYYDAIWAFANNQLIVSGPNGTAGIFATYPSGHLDMVNGFFDQFIGTASLIVCVLAIVDPNNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNPARDFGPRLFTAIAGWGSEVFTTGRHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEP--PPPSTDEENVKLSQVKHKE-->Horse/1-292MGRQKELVSRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPIYTLAQTLGAFLGAGIIFGLYYDAIWAFANNQLIVSGPNGTAGIFATYPSGHLDMVNGFFDQFIGTAALIVCVLAIVDPYNNPVPRGLQAFTVGLVVLVIGTSMGFNSGYAVNPARDFGPRLFTAIAGWGSEVFTTGRHWWWVPIISPLLGSIAGVFVYQLMIGCHLEQ--PPPSTEQENVKLAHVKHKEQI>Dog/1-292MGRQKELVSRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPVYALAQTLGAFLGAGIVFGLYYDAIWDFAKNELVVSGPNGTAGIFATYPSGHLDMVNGFFDQFIGTASLIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNPARDFGPRLFTAIAGWGSEVFTTGRHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEQ--PPSSTEQENVKLAHVKHKEQI>Mouse/1-292MGRQKELMNRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPIYALAQTLGAFLGAGIVFGLYYDAIWAFANNELFVSGPNGTAGIFATYPSGHLDMVNGFFDQFIGTAALIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNPARDFGPRLFTALAGWGSEVFTTGRHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEQ--PPPSTEEENVKLAHMKHKEQI>Rat/1-292MGRQKELMNRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLAILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPIYTLAQTLGAFLGAGIVFGLYYDAIWAFAGNELVVSGPNGTAGIFATYPSGHLDMVNGFFDQFIGTAALIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNPARDFGPRLFTALAGWGSEVFTTGQNWWWVPIVSPLLGSIGGVFVYQLMIGCHLEQ--PPPSTEAENVKLAHMKHKEQI>Chicken/1-292MGRQKDVLATIEEHLRIRNKLVRQALAECLGTLILVLFGCGSVAQIVLSRGTHGGFLTVNLAFGFAVMLGILIAGQVSGGHLNPAVTFAMCFLAREPWIKLPVYALAQTLGAFLGAGIVFGLYHDAIWAFGSNHLYVTGENATAGIFATYPSQHLNVVNGFFDQFIGTASLIVCVLAIVDPFNNPVPPGLEAFTVGFVVLVIGTSMGFYSGYAVNPARDFGPRLFTAIAGWGTEVFWTGKQWWWVPIVAPFLGAIAGVIVYQLMIGCHDEP--SPPASEQETVKLANVKHKERV>Frog/1-294MGRQKDFINKCNQLLRLRNKLLRQALSECLGTLILVMFGCGSVAQVVLSKGSHGQFLTVNLAFGFAVMLGILISGQVSGGHLNPAVTFALCIMAREPWIKFPIYSFAQTLGAFLGAGIIYGLYYDAIWFFGNDQLFVMGENGTAGIFTTFPSEHLTLINGFFDQFIGTAALIVCVLAIVDPNNNPIPRGLEAFTVGFVVLVIGTSMGFNSGYAVNPARDFGPRLFTSLAGWGTEVFWAGNQWWWVPIVSPLLGAFTGVLVYQLMIGCHIEPAQTPQSTEQENIKLADVKNKDRI… 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:10Human/1292 0.000000 0.029038 0.054794 0.062786 0.050998 0.051271 0.047527 0.058924 0.226711 0.264448Monkey/1-2 0.029038 0.000000 0.054409 0.062342 0.050616 0.043780 0.047020 0.062200 0.216003 0.260350Cow/1-292 0.054794 0.054409 0.000000 0.014360 0.039421 0.050476 0.050841 0.069528 0.212661 0.269528Pig/1-290 0.062786 0.062342 0.014360 0.000000 0.039782 0.050941 0.055094 0.074030 0.211011 0.267450Horse/1-29 0.050998 0.050616 0.039421 0.039782 0.000000 0.039464 0.039726 0.054616 0.223549 0.264562Dog/1-292 0.051271 0.043780 0.050476 0.050941 0.039464 0.000000 0.039882 0.054988 0.210443 0.279946Mouse/1-29 0.047527 0.047020 0.050841 0.055094 0.039726 0.039882 0.000000 0.028945 0.222880 0.261103Rat/1-292 0.058924 0.062200 0.069528 0.074030 0.054616 0.054988 0.028945 0.000000 0.239230 0.278508Chicken/1- 0.226711 0.216003 0.212661 0.211011 0.223549 0.210443 0.222880 0.239230 0.000000 0.266608Frog/1-294 0.264448 0.260350 0.269528 0.267450 0.264562 0.279946 0.261103 0.278508 0.266608 0.000000Question 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 13Alpha AACGUGGCCAAAUBeta AAGGUCGCCAAACGamma CAUUUCGUCACAADelta GGUAUUUCGGCCUEpsilon GGGAUCUCGGCCCRun 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): 5Alpha 0.000000 0.330447 0.625670 1.032032 1.354086Beta 0.330447 0.000000 0.375578 1.096290 0.677616Gamma 0.625670 0.375578 0.000000 0.975798 0.861634Delta 1.032032 1.096290 0.975798 0.000000 0.226703Epsilon 1.354086 0.677616 0.861634 0.226703 0.000000Run 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.Answer: