Discover our collection of 6 research tools and applications for phylogenetics.
Found 6 of 6 tools
Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae). Recovering genes from targeted sequence capture data. Current version: 1.3.1 (August 2018). -- Read our article in Applications in Plant Sciences (Open Access). HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.
PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).
Phylogenetic estimation software using Maximum Likelihood
A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate. TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.
The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org