Hi Arman,

As other people suggested, all the explanation should be in the legend of the figure. Often, the number on the scale should be the percentage of genetic variation. For example, if this was the case of your figure, the scale would suggest a 0.2 (20%) genetic variation for the length of the scale. However, in this case you would not be able to have a total distance >1. For phylogenetic studies, this length would be usually much shorter, with a scale bar at about 2-5%. However, this is not always the case, and that's why scale bars should always be explained under the figures.

In your example, "number of differences between the sequences" is to say the least incomplete (and it is not your fault for not understanding). They may be referring to something they explained better in the text? Maybe "differences" is referring to specific sites in the protein?

Also, just to be sure it is clear, I showed in the figure how to calculate the distance between the proteins. You have to consider the full length of both the branches up to the point these are connected (in RED in the attached figure). In your case, the branches A-1 and B-4 are connected only at the base of the tree. Therefore the distance between them is APPROXIMATELY 12 times the scale bar, or 2.4 "differences". In case you need a more precise measurement, however, you would need to create a distance matrix using the sequences that have been used to generate the tree.

Hope this will be helpful!

You will find out by running a BLAST between the two proteins.

Yes, that can be done. However, I already have an evolutionary tree. So, instead of checking one by one via BLAST, it should be possible to infer from the tree which proteins are close to each other, isn't it?

to get the distance between them, you simply sum up the length of the branches between them, i.e., you sum the horisontal branches leading from one of them to the root and then do the same for the other.

The answer depends on whether you want to know how divergent the sequences are from one another (which can be measured by branch lengths), or whether the sequences share some phylogenetic affinity (they are in different clades).

Dear Rex, thank you for your answer.

I would like to know how divergent the sequences are from one another. As you suggested I can do that by measuring branch length. But what does 0.2 represent? Let's say, I measured the branch length and the result is 1.2. What is the unit of the scale?

Hello Arman,

I would assume that the author(s) would have mentioned that in the Methods, if not the Results section. Are these sequences DNA or Amino Acid sequences? For DNA, the distances could be a simple percentage difference between the two sequences ('uncorrected p) or some more refined algorithm (e.g., one-parameter, two-parameter, or likelihood models). In each case, the distance is often expressed as 'percent divergence.' There are other estimates for Amino Acid sequences, but I am less familiar with those.

I hope this helps.

Rex.

Check the figure legend for the units on the scale bar. It is likely amino acid substitutions per something, but as Rex said, you need to find that.

Hi Arman,

As other people suggested, all the explanation should be in the legend of the figure. Often, the number on the scale should be the percentage of genetic variation. For example, if this was the case of your figure, the scale would suggest a 0.2 (20%) genetic variation for the length of the scale. However, in this case you would not be able to have a total distance >1. For phylogenetic studies, this length would be usually much shorter, with a scale bar at about 2-5%. However, this is not always the case, and that's why scale bars should always be explained under the figures.

In your example, "number of differences between the sequences" is to say the least incomplete (and it is not your fault for not understanding). They may be referring to something they explained better in the text? Maybe "differences" is referring to specific sites in the protein?

Also, just to be sure it is clear, I showed in the figure how to calculate the distance between the proteins. You have to consider the full length of both the branches up to the point these are connected (in RED in the attached figure). In your case, the branches A-1 and B-4 are connected only at the base of the tree. Therefore the distance between them is APPROXIMATELY 12 times the scale bar, or 2.4 "differences". In case you need a more precise measurement, however, you would need to create a distance matrix using the sequences that have been used to generate the tree.

Hope this will be helpful!

Dear Francesco,

Thank you very much for your detailed answer and for your time. I really appreciate your help.

Have a great day!

Arman