1983 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 while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the firs...1955 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-spe...1868 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 r...1853 days ago
FUMA GWAS: Functional Mapping and Annotation of Genome-Wide Association Studies
FUMA is a platform that can be used to annotate, prioritize, visualize and interpret GWAS results. The SNP2GENE function takes GWAS summary statistics as an i...1852 days ago
1835 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid w...1772 days ago
ALF--a simulation framework for genome evolution.
Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A descr...1709 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used...1662 days ago
StringTie Transcript assembly and quantification for RNA-Seq
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional ...1478 days ago