Hepatitis delta virus genetic variability: from genotypes I, II, III to eight major clades?
P Deny - Hepatitis delta virus, 2006 - Springer
Hepatitis D virus (HDV) is a satellite of hepatitis B virus (HBV) for transmission and
propagation, and infects nearly 20 million people worldwide. The HDV genome is composed …
propagation, and infects nearly 20 million people worldwide. The HDV genome is composed …
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and
comparative genomics studies. However, from the same set of sequences different MSAs …
comparative genomics studies. However, from the same set of sequences different MSAs …
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
G Talavera, J Castresana - Systematic biology, 2007 - academic.oup.com
Alignment quality may have as much impact on phylogenetic reconstruction as the
phylogenetic methods used. Not only the alignment algorithm, but also the method used to …
phylogenetic methods used. Not only the alignment algorithm, but also the method used to …
The amphibian tree of life
The evidentiary basis of the currently accepted classification of living amphibians is
discussed and shown not to warrant the degree of authority conferred on it by use and …
discussed and shown not to warrant the degree of authority conferred on it by use and …
GUIDANCE: a web server for assessing alignment confidence scores
Evaluating the accuracy of multiple sequence alignment (MSA) is critical for virtually every
comparative sequence analysis that uses an MSA as input. Here we present the GUIDANCE …
comparative sequence analysis that uses an MSA as input. Here we present the GUIDANCE …
Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation
T Lefébure, CJ Douady, M Gouy, J Gibert - Molecular phylogenetics and …, 2006 - Elsevier
With today's technology for production of molecular sequences, DNA taxonomy and
barcoding arose as a new tool for evolutionary biology and ecology. However, their validities …
barcoding arose as a new tool for evolutionary biology and ecology. However, their validities …
Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling
Considerable research efforts have focused on elucidating the systematic relationships
among salmonid fishes; an understanding of these patterns of relatedness will inform …
among salmonid fishes; an understanding of these patterns of relatedness will inform …
An alignment confidence score capturing robustness to guide tree uncertainty
Multiple sequence alignment (MSA) is the basis for a wide range of comparative sequence
analyses from molecular phylogenetics to 3D structure prediction. Sophisticated algorithms …
analyses from molecular phylogenetics to 3D structure prediction. Sophisticated algorithms …
A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion
B Misof, K Misof - Systematic biology, 2009 - academic.oup.com
Random similarity of sequences or sequence sections can impede phylogenetic analyses or
the identification of gene homologies. Additionally, randomly similar sequences or …
the identification of gene homologies. Additionally, randomly similar sequences or …
Diversity and host specificity of endophytic Rhizoctonia‐like fungi from tropical orchids
JT Otero, JD Ackerman… - American Journal of Botany, 2002 - Wiley Online Library
All orchids have an obligate relationship with mycorrhizal symbionts. Most orchid
mycorrhizal fungi are classified in the form‐genus Rhizoctonia. This group includes …
mycorrhizal fungi are classified in the form‐genus Rhizoctonia. This group includes …