phylotree

phylotree assesses congruence between two phylogenetic trees derived from sequence alignments by comparing distributions of phylogenetic trees to test for significant incongruence.

Key Features:

• Distribution-based comparison: Compares distributions of phylogenetic trees rather than individual tree estimates.
• Vector-space embedding: Maps phylogenetic trees into a vector space to enable statistical comparison.
• Difference-of-means test: Evaluates distributional differences using the difference of means as the test statistic.
• Kernel-based distance computation: Employs a kernel method to compute distances between means in high-dimensional feature spaces.
• Feature spaces (splits or quartets): Supports high-dimensional feature spaces defined by splits or quartets.
• Bootstrap significance: Generates p-values by bootstrapping alignment columns.
• Detection of genomic events: Aids identification of horizontal gene transfer and reshuffling in gene tree analyses.
• Validation on simulated data: Validated using simulated datasets under a coalescence model.

Scientific Applications:

• Gene tree incongruence testing: Tests congruence among gene trees to identify significant incongruence and putative horizontal gene transfer or reshuffling events.
• Cophylogeny studies: Applied to host–parasite cophylogeny analyses such as gophers and lice.
• Plant–symbiont systems: Applied to analyses of grasses with endophytes.
• Fungal genomics: Applied to comparisons among multiple fungal genes from the same genome.

Methodology:

Phylogenetic trees are mapped into a vector space, distributions are compared using the difference of means, distances between means are computed with a kernel method in high-dimensional feature spaces (e.g., splits or quartets), and p-values are obtained by bootstrapping alignment columns.