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Letter: TreeAdder: a tool to assist the optimal positioning of a new leaf into an existing phylogenetic tree [PDF]
, 2007 TreeAdder is a computer application that adds a leaf in all possible positions on a phylogenetic tree. The resulting set of trees represent a dataset appropriate for maximum likelihood calculation of the optimal tree.
Gatherer, Derek
core +1 more source
Rearrangement operations on unrooted phylogenetic networks
Theory and Applications of Graphs, 2019 Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and ...
Remie Janssen, Jonathan Klawitter
doaj +1 more source
Mitochondrial DNA. Part B. Resources, 2021 We determined a complete mitochondrial genome of Episoriculus leucops. This mitogenome is a circular molecule with 16,838 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA).
Dan Chen +4 more
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Molecular biology and evolution, 2019 Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different ...
Li-Gen Wang +13 more
semanticscholar +1 more source
Cancer phylogenetic tree inference at scale from 1000s of single cell genomes
bioRxiv, 2020 A new generation of scalable single cell whole genome sequencing (scWGS) methods allows unprecedented high resolution measurement of the evolutionary dynamics of cancer cell populations.
Sohrab Salehi +14 more
semanticscholar +1 more source
Using PhyloSuite for molecular phylogeny and tree‐based analyses
iMeta, 2023 Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced researchers, conquering the large number of software programs required for a multilocus‐based phylogenetic reconstruction can be somewhat daunting and time‐consuming ...
Chuan-Yu Xiang +8 more
semanticscholar +1 more source
A new resolution function to evaluate tree shape statistics.
PLoS ONE, 2019 Phylogenetic trees are frequently used in biology to study the relationships between a number of species or organisms. The shape of a phylogenetic tree contains useful information about patterns of speciation and extinction, so powerful tools are needed ...
Maryam Hayati +2 more
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Understanding the tree of life: an overview of tree-reading skill frameworks
Evolution: Education and Outreach, 2019 Diagrammatic depictions of evolutionary relationships play an increasingly important role in scientific and educational literature. Reading evolutionary trees is seen as a major challenge for biologists in learning about evolution and its applications in
Thilo Schramm +2 more
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Novel metric for hyperbolic phylogenetic tree embeddings
bioRxiv, 2020 Advances in experimental technologies such as DNA sequencing have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of ...
Hirotaka Matsumoto +2 more
semanticscholar +1 more source
The Fair Proportion is a Shapley Value on phylogenetic networks too
, 2018 The Fair Proportion of a species in a phylogenetic tree is a very simple measure that has been used to assess its value relative to the overall phylogenetic diversity represented by the tree.
Coronado, Tomás M. +2 more
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