Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment

Abstract

We introduce a graphical method, likelihood-mapping, to visualize the phylogenetic content of a set of aligned sequences. The method is based on an analysis of the maximum likelihoods for the three fully resolved tree topologies that can be computed for four sequences. The three likelihoods are represented as one point inside an equilateral triangle. The triangle is partitioned in different regions. One region represents star-like evolution, three regions represent a well-resolved phylogeny, and three regions ref lect the situation where it is difficult to distinguish between two of the three trees. The location of the likelihoods in the triangle defines the mode of sequence evolution. If n sequences are analyzed, then the likelihoods for each subset of four sequences are mapped onto the triangle. The resulting distribution of points shows whether the data are suitable for a phylogenetic reconstruction or not.

Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses

“…Analyses were performed using quartet sampling and a neighbor-joining tree with 10,000 randomly chosen quartets (Strimmer and von Haeseler, 1997). This result provides a simple but versatile approach to visualize a summary of phylogenetic content of a dataset and the relative frequencies of the likelihoods for each topology represented as one point inside an equilateral triangle.…”

Phylogeny and DNA barcoding of inquiline oak gallwasps (Hymenoptera: Cynipidae) of the Western Palaearctic

“…Likelihood mapping (Strimmer & von Haeseler, 1997) provides an estimate of the phylogenetic utility of a set of sequences, and was performed in TreePuzzle 5.0 (Schmidt et al, 2002) using the HKY model of nucleotide substitution. Likelihood maps were constructed 340 for each gene with parameters estimated from the data set and using all possible quartets of taxa.…”

Genetic clustering of recent classical swine fever virus isolates from Karnataka, India revealed the emergence of subtype 2.2 replacing subtype 1.1

“…Nucleotide divergence/similarity was calculated for all the three regions using Megalign module of Lasergene package (DNASTAR Inc., USA). The transition/transversion (Ts/ Tv) rate was estimated from the dataset using TreePuzzle, Ver.5.2 [25]. The bootstrap values were calculated with the modules SEQBOOT, DNADIST, NEIGHBOR and CON-SENSE of the PHYLIP Ver.…”