Insertions and deletions: Computational methods, evolutionary dynamics, and biological applications
Insertions and deletions constitute the second most important source of natural genomic
variation. Insertions and deletions make up to 25% of genomic variants in humans and are …
variation. Insertions and deletions make up to 25% of genomic variants in humans and are …
Three roads diverged? Routes to phylogeographic inference
EW Bloomquist, P Lemey, MA Suchard - Trends in Ecology & Evolution, 2010 - cell.com
Phylogeographic methods facilitate inference of the geographical history of genetic
lineages. Recent examples explore human migration and the origins of viral pandemics …
lineages. Recent examples explore human migration and the origins of viral pandemics …
Testing the use of ITS rDNA and protein-coding genes in the generic and species delimitation of the lichen genus Usnea (Parmeliaceae, Ascomycota)
In lichen-forming fungi, traditional taxonomical concepts are frequently in conflict with
molecular data, and identifying appropriate taxonomic characters to describe phylogenetic …
molecular data, and identifying appropriate taxonomic characters to describe phylogenetic …
Molecular homology and multiple-sequence alignment: an analysis of concepts and practice
DA Morrison, MJ Morgan… - Australian Systematic …, 2015 - CSIRO Publishing
Sequence alignment is just as much a part of phylogenetics as is tree building, although it is
often viewed solely as a necessary tool to construct trees. However, alignment for the …
often viewed solely as a necessary tool to construct trees. However, alignment for the …
Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data
The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed
based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank …
based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank …
Is sequence alignment an art or a science?
DA Morrison - Systematic Botany, 2015 - ingentaconnect.com
Aligning multiple nucleotide sequences is a prerequisite for many if not most comparative
sequence analyses in evolutionary biology. These alignments are often recognized as …
sequence analyses in evolutionary biology. These alignments are often recognized as …
Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs
Background A standard procedure in many areas of bioinformatics is to use a single multiple
sequence alignment (MSA) as the basis for various types of analysis. However, downstream …
sequence alignment (MSA) as the basis for various types of analysis. However, downstream …
Phylogenetic relationships of Pieridae (Lepidoptera: Papilionoidea) in China based on seven gene fragments
C Ding, Y Zhang - Entomological Science, 2017 - Wiley Online Library
The butterfly family Pieridae includes approximately 1000 described extant species
distributed worldwide. Among these, 154 species belonging to 24 genera are recorded in …
distributed worldwide. Among these, 154 species belonging to 24 genera are recorded in …
Generalized bootstrap supports for phylogenetic analyses of protein sequences incorporating alignment uncertainty
M Chatzou, EW Floden, P Di Tommaso… - Systematic …, 2018 - academic.oup.com
Phylogenetic reconstructions are essential in genomics data analyses and depend on
accurate multiple sequence alignment (MSA) models. We show that all currently available …
accurate multiple sequence alignment (MSA) models. We show that all currently available …
Multiple sequence alignment is not a solved problem
DA Morrison - arXiv preprint arXiv:1808.07717, 2018 - arxiv.org
Multiple sequence alignment is a basic procedure in molecular biology, and it is often
treated as being essentially a solved computational problem. However, this is not so, and …
treated as being essentially a solved computational problem. However, this is not so, and …