CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall. Please not...762 days ago
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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 pha...388 days ago
PhyloHerb: A highâthroughput phylogenomic pipeline for processing genome skimming data
Phylogenomic Analysis Pipeline for Herbarium Specimens What is PhyloHerb: Phylo...As (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a...e (5x cpDNA) plastome phylogeny, recycling plastid genes from...294 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 inf...126 days ago
PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens
What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming&nbs...As (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a...e (5x cpDNA) plastome phylogeny, recycling plastid genes from...126 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 famili...125 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 classif...to SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so t...113 days ago