Phylogenetic tree building in the genomic age
Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …
Statistics and truth in phylogenomics
Phylogenomics refers to the inference of historical relationships among species using
genome-scale sequence data and to the use of phylogenetic analysis to infer protein …
genome-scale sequence data and to the use of phylogenetic analysis to infer protein …
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 …
[图书][B] Bayesian evolutionary analysis with BEAST
AJ Drummond, RR Bouckaert - 2015 - books.google.com
What are the models used in phylogenetic analysis and what exactly is involved in Bayesian
evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you …
evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you …
Phylogeny-aware alignment with PRANK
A Löytynoja - Multiple sequence alignment methods, 2014 - Springer
Evolutionary analyses require sequence alignments that correctly represent evolutionary
homology. Evolutionary and structural homology are not the same and sequence alignments …
homology. Evolutionary and structural homology are not the same and sequence alignments …
[PDF][PDF] Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria
Alkatib, S., Scharff, LB, Rogalski, M., Fleischmann, TT, Matthes, A., Seeger, S., Schöttler, MA,
Ruf, S. & Bock, R.(2012) The contributions of wobbling and superwobbling to the reading of …
Ruf, S. & Bock, R.(2012) The contributions of wobbling and superwobbling to the reading of …
Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference
Phylogenetic inference is generally performed on the basis of multiple sequence alignments
(MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong …
(MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong …
SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees
Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part
because multiple sequence alignments must be accurate for phylogeny estimation methods …
because multiple sequence alignments must be accurate for phylogeny estimation methods …
Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular
sequence data sets from large numbers of species. However, this task is often difficult, slow …
sequence data sets from large numbers of species. However, this task is often difficult, slow …
Fast statistical alignment
We describe a new program for the alignment of multiple biological sequences that is both
statistically motivated and fast enough for problem sizes that arise in practice. Our F ast S …
statistically motivated and fast enough for problem sizes that arise in practice. Our F ast S …