tag:blogger.com,1999:blog-36768584.post8601996316834540722..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Admitting to Ignorance on Interpreting Bootstrap ValuesKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-36768584.post-77673125929065106932015-12-17T05:57:15.641-05:002015-12-17T05:57:15.641-05:00To the best of my knowledge, the correct interpret...To the best of my knowledge, the correct interpretation is - as said above - the fraction of bootstrap replicates which support the split of the subtree rooted at the child node of the branch from the rest of the tree.<br /><br />Split 2 is meaningless without some indication of what outgroup determined the root. If there was no outgroup, then the value of 1.0 is some default assigned by the program so that all internal branches have bootstrap values.<br />Toby Sargeanthttps://www.blogger.com/profile/17505092553510232102noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-66495200358577670592015-11-30T11:23:08.543-05:002015-11-30T11:23:08.543-05:00The way I think of it is to collapse poorly suppor...The way I think of it is to collapse poorly supported nodes, which would create a polytomy between A-D, E and F-G. That would mean that it's possible that E groups with A-D, but also possible that F-G groups with A-D (making E basal to all the other taxa). <br /><br />HOWEVER, it is pretty unusual to have different bootstrap values on each side of the basal split like that. Most algorithms infer unrooted trees which can then be drawn with whatever root you like, and in a unrooted tree A-D vs E-G is a single bipartition, so it should have a single bootstrap value. I guess you must of used some rooted tree method...Heathhttps://www.blogger.com/profile/05032127727876717194noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-1229390944898618012015-11-30T09:50:58.403-05:002015-11-30T09:50:58.403-05:00It would be useful to know what methods/software y...It would be useful to know what methods/software you are using, as there's some guesswork involved otherwise. However, I think the key point is to think of bootstraps as being associated with "clustering" rather than "splitting". Despite how they are drawn in your figures, they are associated with branches, not nodes. They indicate what proportion of bootstrap replicate trees that branch exists in. So 99.6% of trees clustered F and G, but only 83.5% clustered E,F and G. Presumably, in most of the other replicates E was positioned on the other side of the root, outside of the ABCD cluster.Royhttps://www.blogger.com/profile/12895032436551237930noreply@blogger.com