Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
..., Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top–down manner. And along a guided tree, it iteratively merges siblin...2019 days ago
Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
...protein-coding genes have been reconstructed for 78 genomes of now-extinct species that were the common ancestors of extant species from across the tree of life.2005 days ago
visNetwork: an R package for network visualization, using vis.js javascript library
...eractivity controls (highlight, collapsed nodes, selection, zoom, physics, movement of nodes, tooltip, events, …) visualize rpart tree...1937 days ago
genoPlotR - plot gene and genome maps project!
...segments on the plot Add annotations to all the lines Create smart, automatic annotations for genomes, based on gene names Add a user-generated tree Add a global scale or a scal...1965 days ago
1935 days ago
UPhO: Scripts for homology and orthology assessment from genomic sequences.
...h and without inparalogs from input gene family trees. Refer to the Documentation....elp. The only input requierement for UPhO is a tree (or trees) in Newick format i...t custom delimiters can be defined. Examples of trees to test UPhO are provided in...1932 days ago
IQ-TREE: Efficient software for phylogenomic inference
...ochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML a...elihoods with similar computing time IQ-TREE found higher likelihoods betw...of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%....1897 days ago
ALF--a simulation framework for genome evolution.
Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of...1650 days ago
1615 days ago
3D de novo assembly (3D DNA) pipeline
For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aiden...1548 days ago