A scale-free method for testing the proportionality of branch lengths between two phylogenetic trees
نویسندگان
چکیده
We introduce a scale-free method for testing the proportionality of branch lengths between two phylogenetic trees that have the same topology and contain the same set of taxa. This method scales both trees to a total length of 1 and sums up the differences for each branch. Compared to previous methods, ours yields a fully symmetrical score that measures proportionality without being affected by scale. We call this score the normalized tree distance (NTD). Based on real data, we demonstrate that NTD scores are distributed unimodally, in a manner similar to a log-normal distribution. The NTD score can be used to, for example, detect co-evolutionary processes and measure the accuracy of branch length estimates.
منابع مشابه
Statistical method for estimating the standard errors of branch lengths in a phylogenetic tree reconstructed without assuming equal rates of nucleotide substitution among different lineages.
A statistical method is developed for estimating the standard errors of branch lengths in a phylogenetic tree reconstructed without assuming equal rates of nucleotide substitution among different lineages. This method can be easily used for testing whether the length of an interior branch in a reconstructed tree is positive, i.e., whether the topology of the tree is correct. Computer simulation...
متن کاملA Simple Method for Estimating and Testing Minimum-Evolution
A simple method for estimating and testing phylogenetic trees under the principle of minimum evolution (ME) is presented. The basic procedure of this method is first to obtain the neighbor-joining (NJ) tree by Saitou and Nei’s method and then to search for a tree with the minimum value of the sum (S) of branch lengths by examining all trees that are closely related to the NJ tree. Once the ME t...
متن کاملThe K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees
SUMMARY We introduce a new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees. To do this, the algorithm first scales one of the trees to have a global divergence as similar as possible to the other tree. Then, the branch length distance, which takes differences in topology and branch lengths into account, is app...
متن کاملNumerical Algebraic Geometry for Analysis of Phylogenetic Trees
Using tools from numerical algebraic geometry, we propose a phylogenetic reconstruction algorithm which uses the distance to the nearest point on the phylogenetic model to select the tree of best fit. This method allows for the reconstruction of branch lengths and for hypothesis testing. A data-dependent statistical test identifies correctly reconstructed quartet trees 100% of the time when the...
متن کاملBootstrap method of interior-branch test for phylogenetic trees.
Statistical properties of the bootstrap test of interior branch lengths of phylogenetic trees have been studied and compared with those of the standard interior-branch test in computer simulations. Examination of the properties of the tests under the null hypothesis showed that both tests for an interior branch of a predetermined topology are quite reliable when the distribution of the branch l...
متن کامل