homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated ver...man, W.A., Johnson, M.G., and C.J. Rothfels. 2022. Homologizer: phylogenetic ph...381 days ago
PhyloHerb: A highâthroughput phylogenomic pipeline for processing genome skimming data
Phylogenomic Analysis Pipeline for Herbarium Specimens What is PhyloHerb: PhyloH...NAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a...ge (5x cpDNA) plastome phylogeny, recycling plastid genes from...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 straightforwar...ny additional ortholog alignments can be generated from multi-copy gene fam...retain high-quality alignments for phylogenetic in...118 days ago
PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens
What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming ...NAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a...ge (5x cpDNA) plastome phylogeny, recycling plastid genes from...118 days ago
OMArk: software for proteome (protein-coding gene repertoire) quality assessment
OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides mea...acterizes the consistency of all protein coding genes with regard to their homolog...oftware for fast placement of all proteins into gene famil...118 days ago
doubletrouble: identify duplicated genes from whole-genome protein sequences and classify
doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify...nto SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so...105 days ago
bacLIFE: an automated genome mining tool for identification of lifestyle associated genes
bacLIFE is a streamlined computational workflow that annotates bacterial genom...terial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and biosynthetic gen...e Predicts, clusters and annotates the genes of e...95 days ago
SeqCAT: Sequence Conversion and Analysis Toolbox
Your all-in-one solution for smooth conversion of sequence coordinates. Designed for...simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate sequences, and easily validate complex genetic ev...4 days ago