OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users from over 60 countries.413 days ago
394 days ago
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-y287 days ago
PhyloHerb: A highâthroughput phylogenomic pipeline for processing genome skimming data
...blies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a species tree. It is designed to be a...286 days ago
138 days ago
PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens
...blies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a species tree. It is designed to be a...118 days ago
OMArk: software for proteome (protein-coding gene repertoire) quality assessment
...characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orth...118 days ago
ExRec: Exclusion of Recombined DNA
...in the package convert the recombination-filtered data into single-locus NEXUS or PHYLIP files. The ExRec package can thus facilitate species delimitation, species tree, and historical demograp...82 days ago
Bactopia: a flexible pipeline for complete analysis of bacterial genomes
...sp;and Bactopia Tools, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on Lactobacillus crispatus, a species that is a common part of the...10 days ago