Algorithm of OMA for large-scale orthology inference
Background OMA is a project that aims to identify orthologs within publicly available,
complete genomes. With 657 genomes analyzed to date, OMA is one of the largest projects …
complete genomes. With 657 genomes analyzed to date, OMA is one of the largest projects …
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference
Motivation Accurate orthology inference is a fundamental step in many phylogenetics and
comparative analysis. Many methods have been proposed, including OMA (Orthologous …
comparative analysis. Many methods have been proposed, including OMA (Orthologous …
Controversies in modern evolutionary biology: the imperative for error detection and quality control
Background The data from high throughput genomics technologies provide unique
opportunities for studies of complex biological systems, but also pose many new challenges …
opportunities for studies of complex biological systems, but also pose many new challenges …
Support patterns from different outgroups provide a strong phylogenetic signal
It is known that the accuracy of phylogenetic reconstruction decreases when more distant
outgroups are used. We quantify this phenomenon with a novel scoring method, the …
outgroups are used. We quantify this phenomenon with a novel scoring method, the …
Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise
Background The estimation of a distance between two biological sequences is a
fundamental process in molecular evolution. It is usually performed by maximum likelihood …
fundamental process in molecular evolution. It is usually performed by maximum likelihood …
Évolution du VIH: méthodes, modèles et algorithmes
M Jung - 2012 - theses.hal.science
La donnée de séquences nucléotidiques permet d'inférer des arbres phylogénétiques, ou
phylogénies, qui décrivent leurs liens de parenté au cours de l'évolution. Associer à ces …
phylogénies, qui décrivent leurs liens de parenté au cours de l'évolution. Associer à ces …
Codon-based Models of Evolution and Applications in Mammalian Phylogeny
A Schneider - 2009 - research-collection.ethz.ch
Many applications and analyses in computational biology require a model to describe the
evolutionary process at the level of DNA or protein sequences. Typically a Markov model is …
evolutionary process at the level of DNA or protein sequences. Typically a Markov model is …
Fast and accurate estimation of the covariance between pairwise maximum likelihood distances
M Gil - PeerJ, 2014 - peerj.com
Pairwise evolutionary distances are a model-based summary statistic for a set of molecular
sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree …
sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree …
Estimating the difference of means with imputation of the missing observations
CN Bouza, DC Melgar - Investigación Operacional, 2009 - dialnet.unirioja.es
We consider the use of a finite population model for estimating the difference of the means of
two variables under a mechanism for missing observations. The information available on the …
two variables under a mechanism for missing observations. The information available on the …
Evaluating sequence alignments and phylogenies: new methods and large-scale comparisons
M Gil - 2010 - research-collection.ethz.ch
Phylogenetic trees are one of the most important representations of the evolutionary
relationship between genomic sequences. Alternatively, their relatedness can be expressed …
relationship between genomic sequences. Alternatively, their relatedness can be expressed …