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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
TLDR
It is shown that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented and found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. Expand
ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates
TLDR
ModelFinder is presented, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space. Expand
TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
TLDR
TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies. Expand
Ultrafast Approximation for Phylogenetic Bootstrap
TLDR
This work proposes an ultrafast bootstrap approximation approach (UFBoot) to compute the support of phylogenetic groups in maximum likelihood (ML) based trees and offers an efficient and easy-to-use software to perform the UFBoot analysis with ML tree inference. Expand
UFBoot2: Improving the Ultrafast Bootstrap Approximation
TLDR
UFBoot2 is presented, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations and provides suitable bootstrap resampling strategies for phylogenomic data. Expand
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
TLDR
The phylogenetic terrace aware (PTA) data structure is introduced for the efficient analysis under partition models and it is shown that an implementation of PTA in IQ-TREE leads to a substantial speedup of up to 4.5 and 8 times compared with the standard IQ- TREE and RAxML implementations, respectively. Expand
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
TLDR
Some notable features of IQ-TREE version 2 are described and the key advantages over other software are highlighted. Expand
DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA.
TLDR
It is shown that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C-->T and G-->A substitutions, which are due to the occurrence of modified deoxycytidine residues in the template DNA. Expand
Accurate detection of complex structural variations using single molecule sequencing
TLDR
NGMLR and Sniffles perform highly accurate alignment and structural variation detection from long-read sequencing data and can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings. Expand
HaMStR: Profile hidden markov model based search for orthologs in ESTs
TLDR
HaMStR extends in a standardized manner a pre-defined set of orthologs with ESTs from further taxa, and thus provides a comprehensive approach to compile ortholog cluster from any protein coding data. Expand
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