Tools to find similarity between pangenomes.

Provides PhyloXML support for BioRuby.

Pipeline to remove contaminations from EST libraries

Iterate through a samtools pileup file

Iterate through a samtools pileup file

The PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast transit peptides in Plasmodium falciparum. This is an implementation of that algorithm.

Methods for handling multiwell plate annotations, includes ranges and quadrants

Server for polymarker. To be used with cron

Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat

Primer3-related Ruby code - wrappers, Boulder IO, etc.

Bio::Protparam has same interface and function as Bio::Tools::Protparam class of BioPerl, except that it calculate parameters instead of throwing query to Expasy protparam tool.

A toolkit for publishing scientific results and datasets using RDF, OWL, and related technologies

Ruby tools and scripts for QTL mapping, part of the qtlHD project

Just a test

Store relationships in a triple-store, such as gene enrichment and QTL, and use this information for inference and causality

Digests DNA based on restriction enzyme cut patterns

An MCP server that provides access to BioRuby KEGG functionality, allowing AI assistants to query KEGG databases for biological pathways, compounds, and other molecular information.

Provides PhyloXML support for BioRuby. This bioruby-phyloxml gem replaces old unmaintained bio-phyloxml gem.

New Sambamba library comes with a command-line tool for working with SAM/BAM files. This gem brings some of its functionality to Ruby.

Simple classes for parsing SAM, CIGAR and MD:Z strings, including slices. Methods for calling mutations in HGVS format and looking up consequences using Ensembl VEP REST API. Developed for calling mutations at an expected position in an alignment - e.g. Amplicon sequencing of CRISPR-induced mutations.