Re-Mind the Gap! Insertion – Deletion Data Reveal Neglected Phylogenetic Potential of the Nuclear Ribosomal Internal Transcribed Spacer (ITS) of Fungi

Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets

(2012) Johan Bengtsson et al.   RESEARCH IN MICROBIOLOGY

Evolution of the 5.8S nrDNA gene and internal transcribed spacers in Carapichea ipecacuanha (Rubiaceae) within a phylogeographic context

(2011) Camila de Sousa Queiroz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study

(2011) Ester Gaya et al.   MYCOLOGIA

DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context

(2011) Laura J. Kelly et al.   NEW PHYTOLOGIST

Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

(2011) Mark A. Buchheim et al.   PLoS One

Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data

(2011) Zheng Wang et al.   PLoS One

Data Partitions, Bayesian Analysis and Phylogeny of the Zygomycetous Fungal Family Mortierellaceae, Inferred from Nuclear Ribosomal DNA Sequences

(2011) Tamás Petkovits et al.   PLoS One

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

(2010) Dominik Begerow et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Towards realistic benchmarks for multiple alignments of non-coding sequences

(2010) Jaebum Kim et al.   BMC BIOINFORMATICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology

(2010) MARTIN UNTERSEHER et al.   MOLECULAR ECOLOGY

An open source chimera checker for the fungal ITS region

(2010) R. H. NILSSON et al.   Molecular Ecology Resources

A constructive step towards selecting a DNA barcode for fungi

(2010) Ursula Eberhardt   NEW PHYTOLOGIST

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

(2010) Christophe Dessimoz et al.   GENOME BIOLOGY

Phylogenetic inference under varying proportions of indel-induced alignment gaps

(2009) Bhakti Dwivedi et al.   BMC EVOLUTIONARY BIOLOGY

The ITS region as a target for characterization of fungal communities using emerging sequencing technologies

(2009) Rolf Henrik Nilsson et al.   FEMS MICROBIOLOGY LETTERS

Large-Scale Parsimony Analysis of Metazoan Indels in Protein-Coding Genes

(2009) F. Belinky et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny and character evolution of the coprinoid mushroom genus Parasola as inferred from LSU and ITS nrDNA sequence data

(2009) L.G. Nagy et al.   PERSOONIA

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY

The search for the fungal tree of life

(2009) David J. McLaughlin et al.   TRENDS IN MICROBIOLOGY

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

(2008) Ádám Novák et al.   BIOINFORMATICS

A fast structural multiple alignment method for long RNA sequences

(2008) Yasuo Tabei et al.   BMC BIOINFORMATICS

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

(2008) Kazutaka Katoh et al.   BMC BIOINFORMATICS

Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)

(2008) Martin Ryberg et al.   BMC EVOLUTIONARY BIOLOGY

An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity

(2008) Martin Ryberg et al.   NEW PHYTOLOGIST

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

Incorporating gaps as phylogenetic characters across eight DNA regions: Ramifications for North American Psoraleeae (Leguminosae)

(2007) Ashley N. Egan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION