Bioinformatics Tools

MoGAAAP is a convenience pipeline using existing tools that creates annotated genome assemblies from HiFi (and optionally ultra-long ONT and/or Hi-C) reads for a set of related individuals as well as a related reference genome. Our pipeline is species-agnostic and generates an extensive quality assessment report that can be used for manual filtering and refinement of the assembly and annotation.

Lettuce Structural Database -- A research tool designed to explore Bremia and Lettuce proteins. Search for proteins, analyze interactions, and visualize 3D structures.

Locus Comparative Genomics Visualization Tool -- Visualize genes/proteins in genomic regions and their relationships across genotypes or species, enabling identification of homologs/orthologs and gene diversification events.

EffectorO is a pipeline predicting oomycete effector genes using lineage-specificity and machine learning classifiers. See Nur et al. 2023. EffectorO: motif-independent prediction of effectors in oomycete genomes using machine learning and lineage-specificity. MDPI for more information.

The Lettuce Genome Resource (LGR) was developed as a portal to provide access to genetic and genomic resources for cultivated lettuce and its relatives.

SNP/INDEL Discovery Pipeline based on CAP3 assembly or How to find thousand polymorphic sites in EST assembly in 24 steps.

Genome Visualization tool: Program for Visualizing and Querying Genetic Data.

Genome Visualization tool: designed to display genomes in a linear form and show the relationships between genes.

Graph Drawing tool: designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements).

How to obtain a Distance Matrix File from BLAST search results and use it for sequence clustering analysis. It is designed to display genomes in a linear form and show the relationships between genes.

This script was designed to calculate recombination scores for a set of RILs (Recombination Inbred Lines); it does group (clustering) analysis finding different linkage groups based on raw marker scores.

Pixelirator is a program to draw image by using predefined the configuration and the color schema files. It generates PNG formatted images from text files of data.