ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data....llation, a user's guide, and examples. https://journals.plos.org/ploscompbiol/article...1502 days ago
QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses.
Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as DrugBank&n...lypharmacological treatments. https://academic.oup.com/bioinformatics/advance-article...1488 days ago
wgd—simple command line tools for the analysis of ancient whole-genome duplications
wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides...s researchers in a convenient manner. https://academic.oup.com/bioinformatics/article...1376 days ago
Updated science-wide author databases of standardized citation indicators
There was great interest in the databases of standardized citation metrics across all scientists and scientific disciplines [1], and many scientists urged us to provide...1260 days ago
Pandoc: The universal markup converter
Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. Pandoc is a free and open-source document converter, widely used as a writing tool and as a basis for publishing workflows. More at https://pandoc.org/1196 days ago
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/61467721142 days ago
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads gener...proach that has been successful with short reads. https://academic.oup.com/ve/article...1041 days ago
QuasiModo - Quasispecies Metric Determination on Omics
This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In thi...riant calling results on other similar datasets. https://academic.oup.com/bib/article...1037 days ago
k-mers tutorial - classification and taxonomy
DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, ...976 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phyloge...acterial genomes More at https://academic.oup.com/bioinformatics/advance-article...933 days ago