ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
...nd supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or includin...2277 days ago
DendroPy: a Python library for phylogenetic computing
...is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and s...2214 days ago
BASE: a practical de novo assembler for large genomes using long NGS reads
...ntly to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse valid...2035 days ago
UPhO: Scripts for homology and orthology assessment from genomic sequences.
...and without inparalogs from input gene family trees. Refer to the Documentation.p...only input requierement for UPhO is a tree (or trees) in Newick format in which th...custom delimiters can be defined. Examples of trees to test UPhO are provided in...1947 days ago
IQ-TREE: Efficient software for phylogenomic inference
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with simi...1913 days ago
1631 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features,...1620 days ago
ShinyGO v0.61: Gene Ontology Enrichment Analysis + more
...are annotated based on STRING-db (v.10). In addition, it also produces KEGG pathway diagrams with your genes highlighted, hierarchical clustering trees and networks summarizing over...1442 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
...META files (see Manual) or specific variant information as specified in VAR files (see Manual) and NEWICK files for specifying clonal phylogenetic trees in cancer. SVEngine outpus a...1411 days ago
GToTree: a user-friendly workflow for phylogenomics
GToTree is a user-friendly workflow for phylogenomics intended to give more researchers the capability to create phylogenomic trees. The open-access Bioinformatics Journal publication is available here, and documentation and examples can be found at the wiki here.812 days ago