1987 days ago
Genome assembly forensics: finding the elusive mis-assembly
We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and descr...1982 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
MACSE aligns coding NT sequences with respect to their AA translation w...SE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the unde...1960 days ago
IQ-TREE: Efficient software for phylogenomic inference
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing...1960 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). mu...phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putative functions to gene calls using protein-, virus-,...1873 days ago
Apollo: First instantaneous, collaborative genomic annotation editor available on the Web
Apollo is a plug-in for the JBrowse Genome Viewer. In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elem...tion title to confirm their submission. Gene Ontology (GO) terms are suppo...1857 days ago
FUMA GWAS: Functional Mapping and Annotation of Genome-Wide Association Studies
FUMA is a platform that can be used to annotate, prioritiz...alize and interpret GWAS results. The SNP2GENE function takes GWAS summ...enomic areas identified by lead SNPs. The GENE2FUNC function takes a li...1857 days ago
1840 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbu...nge of dozens of Mb and pseudomolecules with better gene space representation than a B...ygous or autopolyploid genomes. A protocol for generating chromosome-conformation...1777 days ago
1771 days ago