Bioinformatics Tools

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.

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.