homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes....Freyman, W.A., Johnson, M.G., and C.J. Rothfels. 2022. Homologizer: phylogenetic phasing of gene copies int...380 days ago
PhyloHerb: A highâthroughput phylogenomic pipeline for processing genome skimming data
..., nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a...clude low-coverage (5x cpDNA) plastome phylogeny, recycling plastid genes from target enrichment data,...286 days ago
Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes. Our goal was to make it straigh...dditional ortholog alignments can be generated from multi-copy gene fam...ain high-quality alignments for phylogenetic inference. The workflow pr...118 days ago
PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens
..., nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a...clude low-coverage (5x cpDNA) plastome phylogeny, recycling plastid genes from target enrichment data,...118 days ago
OMArk: software for proteome (protein-coding gene repertoire) quality assessment
...MArk is a software for proteome (protein-coding gene repertoire) quality assessmen...acterizes the consistency of all protein coding genes with regard to their homolog...oftware for fast placement of all proteins into gene families.118 days ago
doubletrouble: identify duplicated genes from whole-genome protein sequences and classify
doubletrouble aims to identify duplicated genes from whole-genome protein sequence...o SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assign...105 days ago
bacLIFE: an automated genome mining tool for identification of lifestyle associated genes
...cs to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and biosynthetic gen...Clustering module Predicts, clusters and annotates the genes of every input genome Lifes...95 days ago
SeqCAT: Sequence Conversion and Analysis Toolbox
...boratory work, SeqCAT simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate sequences, and easily validate complex genetic events such as fusions wit...4 days ago