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Ka, Ks and Ka/Ks calculations
By Poonam Mahapatra 3007 days agolonglab.uchicago.edu - gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including...BRAKER: pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and...
By Jit 3004 days agobioinf.uni-greifswald.de - Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction...Sybil
By Jit 2998 days agosybil.sourceforge.net - The Sybil software package provides a primarily web-based front-end to comparative genome datasets warehoused in a chado relational database. It was developed by the bioinformatics department at The Institute for Genomic Research (TIGR) and...Nemo – A stochastic, individual-base, genetically explicit simulation platform
By Jit 2974 days agonemo2.sourceforge.net - A recombination map has been added for all multi-locus traits. The map positions (chromosomal) for neutral markers (e.g. SNPs) and loci under selection (QTLs, deleterious mutations, DMIs) can now be specified explicitly, or set at random....LINKS
By Jit 2940 days agogithub.com - LINKS is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads,...Maq: Mapping and Assembly with Quality
By Jit 2922 days agomaq.sourceforge.net - Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/....e-RGA: enhanced Reference Guided Assembly of Complex Genomes
By Jit 2895 days agojournal.embnet.org - Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredibly low cost compared to Sanger sequencing. Despite this, some old problems have become even more difficult, de novo assembly being on...Structural variation: the hidden genomic treasure
By Jit 2904 days ago Comments (6)Structural variants (SVs) such as deletions, insertions, duplications, inversions and translocations litter genomes and are often associated with gene expression changes and severe phenotypes (ie. genetic diseases in humans).MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs
By Jit 2895 days agogithub.com - MeGAMerge MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs) Description MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any...
