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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (168 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (625 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (786 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (838 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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slacTree: SVG Large Annotated Circular Tree drawing
By Jit 2701 days agogithub.com - A simple, extensible, Perl script for producing figures of large phylogenetic trees. While there are many other tree drawing programs, slacTree was originally written in 2009 to fill a need for producing publication quality figures of circular...I-PV: Interactive Protein Sequence Visualization
By Jit 2701 days agohttp://i-pv.org/ - I-PV is a interactive data visualization software designed for inspection of protein sequences and mutation information. It is mainly used for Genetics and Bioinformatics. So what exactly makes it standout? http://i-pv.org/ipv_recDIYA: a bacterial annotation pipeline for any genomics lab
By Jit 2704 days agosourceforge.net - DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and...DESCHRAMBLER
By Jit 2705 days agogithub.com - DESCHRAMBLER is shown to produce highly accurate reconstructions using data simulation and by benchmarking it against other reconstruction tools You can find the detail of reconstructed data at http://bioinfo.konkuk.ac.kr/DESCHRAMBLER/CoreTracker, a codon reassignment tracker
By Abhimanyu Singh 2705 days agogithub.com - CoreTracker detects evidences of codon reassignment from the protein repertoire of a set of genomes by successively applying different algorithms. It’s a filtering approach that explore all possible reassignments in every genomes from the...Circleator
By Jit 2708 days agogithub.com - The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of...AnnotationSketch
By Jit 2708 days agogenometools.org - The AnnotationSketch module is a versatile and efficient C-based drawing library for GFF3-compatible genomic annotations. It is included in the GenomeTools distribution. Additionally, bindings to...Bio-Graphics-2.37
By Jit 2708 days agosearch.cpan.org - BioPerl modules Bio::Graphics + Bio::DB:GFF and example scripts. It can draw some of the (but not all) feature types GBrowse can draw. This script should contain everything you can probably make use of (e.g. transcripts,...eQuant : energy-based quality assessment of protein
By Shruti Paniwala 2709 days agobiosciences.hs-mittweida.de - Protein structures are of varying quality. Especially, in-silico modeled structures are prone to contain serious errors, which limit the usefulness and reliability of these particular protein structures.eQuant is a service for structure...DarkHorse: a method for genome-wide prediction of horizontal gene transfer
By Jit 2712 days agowww.ncbi.nlm.nih.gov - A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or...
