Exercise: Phylogeny - Answers (Seaview version) - Revision history

Henni: /* Step 14 */

2025-11-26T21:02:38Z

Step 14

← Older revision		Revision as of 23:02, 26 November 2025
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	[[File:Ribosomal_proteins_35-NJ_tree.rerooted+annotated.png]]		[[File:Ribosomal_proteins_35-NJ_tree.rerooted+annotated.png]]

	==Step 14==		==Step 13==
	# The mitochondrial proteins are more closely related to each other than to their respective cytoplasmic counterparts. This could indicate that mitochondria have appeared only once in evolution.		# The mitochondrial proteins are more closely related to each other than to their respective cytoplasmic counterparts. This could indicate that mitochondria have appeared only once in evolution.
	# There are two differences: In the mitochondria, Bovine (cow) is the sister group to Human, while in the cytoplasmic proteins, Mouse+Rat comprise the sister group to Human+Macaque. Also, in the mitochondria, Yeast branches out before Arabidopsis on the way to Human, while in the cytoplasmic proteins, the plants including Arabidopsis branch out (slightly) before the fungi including Yeast. In both aspects, the cytoplasmic tree is more correct.		# There are two differences: In the mitochondria, Bovine (cow) is the sister group to Human, while in the cytoplasmic proteins, Mouse+Rat comprise the sister group to Human+Macaque. Also, in the mitochondria, Yeast branches out before Arabidopsis on the way to Human, while in the cytoplasmic proteins, the plants including Arabidopsis branch out (slightly) before the fungi including Yeast. In both aspects, the cytoplasmic tree is more correct.
	# There are more mutations per time unit in the mitochondrial part of the tree. This is evident from the fact that the horizontal distance between the blue and the green circle is larger in the mitochondrial subtree (by approximately a factor 2). Note that the two blue circles represent the same time point in evolutionary history, as do the two green circles. Note also that the branch lengths are proportional to the number of substitutions (accepted mutations).		# There are more mutations per time unit in the mitochondrial part of the tree. This is evident from the fact that the horizontal distance between the blue and the green circle is larger in the mitochondrial subtree (by approximately a factor 2). Note that the two blue circles represent the same time point in evolutionary history, as do the two green circles. Note also that the branch lengths are proportional to the number of substitutions (accepted mutations).

Henni: /* Step 13 */

2025-11-26T21:00:13Z

Step 13

← Older revision		Revision as of 23:00, 26 November 2025
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	-->		-->

	~~==Step 13==~~
	Here is the annotated tree, with blue circles marking the most recent common ancestor of human and yeast, and the green circles marking the most recent common ancestor of human and mouse:		Here is the annotated tree, with blue circles marking the most recent common ancestor of human and yeast, and the green circles marking the most recent common ancestor of human and mouse:

	[[File:~~Ribosomal_proteins_34~~-NJ_tree.annotated~~-iTOL~~.png]]		[[File:Ribosomal_proteins_35-NJ_tree.rerooted+annotated.png]]

	==Step 14==		==Step 14==

Henni: /* Step 12 */

2025-11-26T20:59:13Z

Step 12

← Older revision		Revision as of 22:59, 26 November 2025
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	==Step 12==		==Step 12==
			<!--
	Here is the rerooted tree made by iTOL:		Here is the rerooted tree made by iTOL:

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	Yes, there is a difference: The tree from iTOL has the mitochondrial tips further to the right, while the tree from Seaview has the mitochondrial tips approximately aligned with the cytoplasmic ones. Note that when you select a branch for rerooting, the exact placement of the root on that branch is arbitrary. iTOL chooses the midpoint of the selected branch, while Seaview chooses a point that is closer to the midpoint of the entire tree. Without external information, it is not possible to say which method is most correct.		Yes, there is a difference: The tree from iTOL has the mitochondrial tips further to the right, while the tree from Seaview has the mitochondrial tips approximately aligned with the cytoplasmic ones. Note that when you select a branch for rerooting, the exact placement of the root on that branch is arbitrary. iTOL chooses the midpoint of the selected branch, while Seaview chooses a point that is closer to the midpoint of the entire tree. Without external information, it is not possible to say which method is most correct.
			-->

	==Step 13==		==Step 13==

Henni: /* Step 11 */

2025-11-26T20:56:23Z

Step 11

← Older revision		Revision as of 22:56, 26 November 2025
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	Here is the rerooted tree made by Seaview:		Here is the rerooted tree made by Seaview:

	[[File:Ribosomal_proteins_35-NJ_tree.rerooted~~-Seaview~~.png]]		[[File:Ribosomal_proteins_35-NJ_tree.rerooted.png]]

	==Step 12==		==Step 12==

Henni: /* Step 11 */

2025-11-26T20:55:24Z

Step 11

← Older revision		Revision as of 22:55, 26 November 2025
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	Here is the rerooted tree made by Seaview:		Here is the rerooted tree made by Seaview:

	[[File:~~Ribosomal_proteins_34~~-NJ_tree.rerooted-Seaview.png]]		[[File:Ribosomal_proteins_35-NJ_tree.rerooted-Seaview.png]]

	==Step 12==		==Step 12==

Henni: /* Step 10 */

2025-11-26T20:42:30Z

Step 10

← Older revision		Revision as of 22:42, 26 November 2025
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	==Step 10==		==Step 10==
	Open the FASTA file with the 35 ribosomal protein sequences in Seaview, make sure <u>Alignment options</u> is set to "clustalo", and align all sequences. Then make an NJ tree (with <u>Ignore all gap sites</u> unchecked) and change the view to "<u>circular</u>".		Open the FASTA file with the 35 ribosomal protein sequences in Seaview, make sure <u>Alignment options</u> is set to "clustalo", and align all sequences. Then make an NJ tree (with <u>Ignore all gap sites</u> unchecked) and change the view to "<u>circular</u>".
			<!--
	'''Note:''' the following pictures are made last year, when the number of cytoplasmic+mitochondrial sequences was 34, not 35. The rabbit has been added since then, but the general picture is the same.		'''Note:''' the following pictures are made last year, when the number of cytoplasmic+mitochondrial sequences was 34, not 35. The rabbit has been added since then, but the general picture is the same.-->

	Here is the result:		Here is the result:

	[[File:~~Ribosomal_proteins_34~~-NJ_tree.unrooted.png]]		[[File:Ribosomal_proteins_35-NJ_tree.unrooted.png]]

	And [[Media:~~Ribosomal_proteins_34~~-NJ_tree.unrooted.newick.txt\|here]] is the unrooted Newick tree file.		And [[Media:Ribosomal_proteins_35-NJ_tree.unrooted.newick.txt\|here]] is the unrooted Newick tree file.

	== Step 11 ==		== Step 11 ==

Henni: /* Step 10 */

2024-11-27T10:41:59Z

Step 10

← Older revision		Revision as of 12:41, 27 November 2024
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	Open the FASTA file with the 35 ribosomal protein sequences in Seaview, make sure <u>Alignment options</u> is set to "clustalo", and align all sequences. Then make an NJ tree (with <u>Ignore all gap sites</u> unchecked) and change the view to "<u>circular</u>".		Open the FASTA file with the 35 ribosomal protein sequences in Seaview, make sure <u>Alignment options</u> is set to "clustalo", and align all sequences. Then make an NJ tree (with <u>Ignore all gap sites</u> unchecked) and change the view to "<u>circular</u>".

	'''Note:''' the following pictures are made last year, when the number of cytoplasmic+mitochondrial sequences was 34, not 35. ~~But~~ the general picture is the same.		'''Note:''' the following pictures are made last year, when the number of cytoplasmic+mitochondrial sequences was 34, not 35. The rabbit has been added since then, but the general picture is the same.

	Here is the result:		Here is the result:

Henni: /* Step 10 */

2024-11-27T10:24:43Z

Step 10

← Older revision		Revision as of 12:24, 27 November 2024
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	Open the FASTA file with the 35 ribosomal protein sequences in Seaview, make sure <u>Alignment options</u> is set to "clustalo", and align all sequences. Then make an NJ tree (with <u>Ignore all gap sites</u> unchecked) and change the view to "<u>circular</u>".		Open the FASTA file with the 35 ribosomal protein sequences in Seaview, make sure <u>Alignment options</u> is set to "clustalo", and align all sequences. Then make an NJ tree (with <u>Ignore all gap sites</u> unchecked) and change the view to "<u>circular</u>".

	'''Note:''' the following pictures are made last year, when the number of cytoplasmic sequences was 34, not 35. But the general picture is the same.		'''Note:''' the following pictures are made last year, when the number of cytoplasmic+mitochondrial sequences was 34, not 35. But the general picture is the same.

	Here is the result:		Here is the result:

Henni: /* Step 10 */

2024-11-26T16:03:37Z

Step 10

← Older revision		Revision as of 18:03, 26 November 2024
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	==Step 10==		==Step 10==
	Open the FASTA file with the 34 ribosomal protein sequences in Seaview, make sure <u>Alignment options</u> is set to "clustalo", and align all sequences. Then make an NJ tree (with <u>Ignore all gap sites</u> unchecked) and change the view to "<u>circular</u>". Here is the result:		Open the FASTA file with the 35 ribosomal protein sequences in Seaview, make sure <u>Alignment options</u> is set to "clustalo", and align all sequences. Then make an NJ tree (with <u>Ignore all gap sites</u> unchecked) and change the view to "<u>circular</u>".

			'''Note:''' the following pictures are made last year, when the number of cytoplasmic sequences was 34, not 35. But the general picture is the same.

			Here is the result:

	[[File:Ribosomal_proteins_34-NJ_tree.unrooted.png]]		[[File:Ribosomal_proteins_34-NJ_tree.unrooted.png]]

	And [[Media:Ribosomal_proteins_34-NJ_tree.unrooted.newick.txt\|here]] is the unrooted Newick tree file.		And [[Media:Ribosomal_proteins_34-NJ_tree.unrooted.newick.txt\|here]] is the unrooted Newick tree file.


	== Step 11 ==		== Step 11 ==

Henni: /* Step 9 */

2024-11-26T14:31:43Z

Step 9

← Older revision		Revision as of 16:31, 26 November 2024
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	# 54 results. <br>Search string: <!-- <tt>name:"ribosomal protein l3" taxonomy:eukaryota fragment:no AND reviewed:yes</tt> --> <tt>(protein_name:"ribosomal protein l3") AND (taxonomy_id:2759) AND (fragment:false) AND (reviewed:true)</tt>		# 54 results. <br>Search string: <!-- <tt>name:"ribosomal protein l3" taxonomy:eukaryota fragment:no AND reviewed:yes</tt> --> <tt>(protein_name:"ribosomal protein l3") AND (taxonomy_id:2759) AND (fragment:false) AND (reviewed:true)</tt>
	# 8 and 27 results, respectively. <br>Search strings: <!-- <tt>name:"ribosomal protein l3" taxonomy:eukaryota fragment:no locations:(location:mitochondrion) AND reviewed:yes</tt> --> <tt>(protein_name:"ribosomal protein l3") AND (taxonomy_id:2759) AND (fragment:false) AND (reviewed:true) AND (cc_scl_term:SL-0173)</tt><br>and <!-- <tt>name:"ribosomal protein l3" taxonomy:eukaryota fragment:no locations:(location:cytoplasm) AND reviewed:yes</tt> --> <tt>(protein_name:"ribosomal protein l3") AND (taxonomy_id:2759) AND (fragment:false) AND (reviewed:true) AND (cc_scl_term:SL-0086)</tt> <br>Under the <u>Download</u> tab in UniProt, select "Download all", "FASTA (canonical)" and "Uncompressed".		# 8 and 27 results, respectively. <br>Search strings: <!-- <tt>name:"ribosomal protein l3" taxonomy:eukaryota fragment:no locations:(location:mitochondrion) AND reviewed:yes</tt> --> <tt>(protein_name:"ribosomal protein l3") AND (taxonomy_id:2759) AND (fragment:false) AND (reviewed:true) AND (cc_scl_term:SL-0173)</tt><br>and <!-- <tt>name:"ribosomal protein l3" taxonomy:eukaryota fragment:no locations:(location:cytoplasm) AND reviewed:yes</tt> --> <tt>(protein_name:"ribosomal protein l3") AND (taxonomy_id:2759) AND (fragment:false) AND (reviewed:true) AND (cc_scl_term:SL-0086)</tt> <br>Under the <u>Download</u> tab in UniProt, select "Download all", "FASTA (canonical)" and "Uncompressed".
	# Then use a plain text editor to combine them. Combined FASTA file is here: [https://teaching.healthtech.dtu.dk/material/22111/~~Ribosomal_proteins_34~~.fasta.txt ~~Ribosomal_proteins_34~~.fasta.txt]		# Then use a plain text editor to combine them. Combined FASTA file is here: [https://teaching.healthtech.dtu.dk/material/22111/Ribosomal_proteins_35.fasta.txt Ribosomal_proteins_35.fasta.txt]

	==Step 10==		==Step 10==