A new pipeline for removing paralogs in target enrichment data
Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing
method that has been increasingly used for phylogenomic studies. Unfortunately, current …
method that has been increasingly used for phylogenomic studies. Unfortunately, current …
Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics
• Premise of the study: Hyb‐Seq, the combination of target enrichment and genome
skimming, allows simultaneous data collection for low‐copy nuclear genes and high‐copy …
skimming, allows simultaneous data collection for low‐copy nuclear genes and high‐copy …
Anchored phylogenomics of angiosperms I: assessing the robustness of phylogenetic estimates
An important goal of the angiosperm systematics community has been to develop a shared
approach to molecular data collection, such that phylogenomic data sets from different focal …
approach to molecular data collection, such that phylogenomic data sets from different focal …
Phylogenomics AND biogeography of Castanea (chestnut) and Hamamelis (witch-hazel)–Choosing between RAD-seq and Hyb-Seq approaches
Hyb-Seq and RAD-seq are well-established high throughput sequencing technologies that
have been increasingly used for plant phylogenomic studies. Each method has its own pros …
have been increasingly used for plant phylogenomic studies. Each method has its own pros …
HybPhyloMaker: target enrichment data analysis from raw reads to species trees
T Fér, RE Schmickl - Evolutionary Bioinformatics, 2018 - journals.sagepub.com
Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is
becoming a standard method of phylogenomics. We developed HybPhyloMaker, a …
becoming a standard method of phylogenomics. We developed HybPhyloMaker, a …
A comprehensive phylogenomic platform for exploring the angiosperm tree of life
The tree of life is the fundamental biological roadmap for navigating the evolution and
properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering …
properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering …
A guide to carrying out a phylogenomic target sequence capture project
T Andermann, MF Torres Jiménez… - Frontiers in …, 2020 - frontiersin.org
High-throughput DNA sequencing techniques enable time-and cost-effective sequencing of
large portions of the genome. Instead of sequencing and annotating whole genomes, many …
large portions of the genome. Instead of sequencing and annotating whole genomes, many …
Bridging the micro‐and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above
Reconstructing phylogenetic relationships at the micro‐and macroevoutionary levels within
the same tree is problematic because of the need to use different data types and analytical …
the same tree is problematic because of the need to use different data types and analytical …
Targeted NGS for species level phylogenomics:“made to measure” or “one size fits all”?
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of
data for inferring multiple, meaningfully resolved, independent gene trees suitable to …
data for inferring multiple, meaningfully resolved, independent gene trees suitable to …
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data
R Ufimov, JM Gorospe, T Fér… - Molecular Ecology …, 2022 - Wiley Online Library
The analysis of target enrichment data in phylogenetics lacks optimization toward using
paralogues for phylogenetic reconstruction. We developed a novel approach of detecting …
paralogues for phylogenetic reconstruction. We developed a novel approach of detecting …