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Performs phylogenetics analyses on trees and sequences. phyx provides a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and Markov Chain Monte Carlo (MCMC) logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets.
ALPHA / Automated Local Phylogenomic Analyses
Serves for automated local phylogenomic analyses. ALPHA’s purpose is to supply implementations for automated analyses in two categories: inference of local genealogies and analyses based on local genealogies for phylogenomic studies. This toolkit has several functionalities for both categories of analyses, allows for multiple import/export features, and is equipped with a graphical user interface for various visualizations of the analyses.
An easy way for ecologists to make realistic, tenable phylogenies. With phyloGenerator, you can download real DNA sequence data for your species of interest, and then generate a calibrated phylogeny using a defensible constraint tree. Your phylogeny may not be 'correct', but it will have branch lengths based on DNA data and its topology will be safe. It'll be a 'real' phylogeny, not a best-guess from taxonomy filled with polytomies. You don't need to have an advanced knowledge of phylogenetics to use phyloGenerator. Just download the program, follow the guide, and you can build a phylogeny in minutes.
A Python package designed to deliver reproducible phylogenomic analyses. ReproPhylo promotes reproducibility on two levels. First, it eases the complex phylogenomic pipeline design process by providing a simple and concise scripting syntax for the execution of complex and forked phylogenetic workflows. Second, it automates reproducibility by employing well trusted containerization, versioning and provenance programs. In ReproPhylo, management of the experiment’s reproducibility and version control is carried out in a ‘frictionless’ manner in the background, without a need for user attention (although users have the option to access and tailor these aspects). Third, it ensures persistence and availability of metadata throughout the workflow, and in all the final products.
Tracks evolution from sequence and serological data. Augur is an informatic processing pipeline that aims to subsamples, cleans, aligns sequences and build a phylogenetic tree from this data. The nextstrain project derives from nextflu, which was specific to influenza evolution. nextstrain is comprised of three components: (i) fauna, a database and IO scripts for sequence and serological data, (ii) augur, informatic pipelines to conduct inferences from raw data, and (iii) auspice, a web app to visualize resulting inferences.
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