Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenetic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies ...

The computation of template matrices is the bottleneck of simple algorithms for perfect phylogeny haplotyping and for perfect phylogeny under mutation and constrained recombination. The fastest algorithms known so far compute them in O(nm) time. In this paper, we describe an algorithm for computing template matrices in O(nm/ log(n)) time. We also present and discuss a conjecture that implies an...

Reconstruction of phylogeny of a protein family from a sequence alignment can produce results of different quality. Our goal is to predict the quality of phylogeny reconstruction basing on features that can be extracted from the input alignment. We used Fitch-Margoliash (FM) method of phylogeny reconstruction and random forest as a predictor. For training and testing the predictor, alignments o...

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker...

MOTIVATION Likelihood-based methods for placing short read sequences from metagenomic samples into reference phylogenies have been recently introduced. At present, it is unclear how to align those reads with respect to the reference alignment that was deployed to infer the reference phylogeny. Moreover, the adaptability of such alignment methods with respect to the underlying reference alignmen...

this study investigated the genetic diversity of morchella species using randomly amplified polymorphic dna markers. morchella species are an important group of edible mushrooms belonging to the family helveliaceae with medicinal and economical significance. in this study we have developed an efficient method of genomic dna isolation which was amplified by eight rapd primers to test the polymor...

the genus ranunculus l., with a worldwide distribution, is the largest member of the ranunculaceae. here, nuclear ribosomal internal transcribed spacer (its) sequence data and chloroplast trnlf sequence data were used to analyze phylogenetic relationships among members of the annual and perennial (group praemorsa, group rhizomatosa, group grumosa and group non-grumosa) species of ranunculus...

Abstract Host phylogeny and environments have all been implicated in shaping the gut microbiota host metabolic traits of mammals. However, few studies evaluated phylogeny-associated microbial assembly plasticity concurrently their relationships on both short-term evolutionary timescales. We reported that branching order dendrogram was nearly congruent with phylogenetic 7 rodent species, this pa...