1958 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
...o contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the unde...1930 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
...tation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putative functions to gene calls using protein-, virus-,...1843 days ago
Apollo: First instantaneous, collaborative genomic annotation editor available on the Web
...s a plug-in for the JBrowse Genome Viewer. In addition to genes and pseudogenes, users can annotate ncRNAs (...prompt users with a publication title to confirm their submission. Gene Ontology (GO) terms are suppo...1827 days ago
FUMA GWAS: Functional Mapping and Annotation of Genome-Wide Association Studies
...ate, prioritize, visualize and interpret GWAS results. The SNP2GENE function takes GWAS summ...ion for all SNPs in genomic areas identified by lead SNPs. The GENE2FUNC function takes a li...1827 days ago
1810 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
...N50 values in the range of dozens of Mb and pseudomolecules with better gene space representation than a B...ed to work on heterozygous or autopolyploid genomes. A protocol for generating chromosome-conformation...1747 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 description of...1683 days ago
phyloXML: XML for evolutionary biology and comparative genomics
...ML (example) is an XML language designed to describe phylogenetic trees (or networks) and as...ides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch...1637 days ago
StringTie Transcript assembly and quantification for RNA-Seq
...e full-length transcripts representing multiple splice variants for each gene locus. Its input can include...ssembled from those reads. In order to identify differentially expressed genes between experiments, StringT...1453 days ago