Assists users to observe DNA and protein sequence data from different species and populations. MEGA is composed of several tools allowing researchers to work on phylogenomics and phylomedicine. This repository includes features aiming to determine gene duplication events in gene family trees. Moreover, this tool is available through a graphical user interface (GUI) and a command line interface.
Provides a suite of utilities that cover a range of complex analysis tasks for immunoglobulin (Ig) repertoire sequencing data. Change-O is a suite of utilities that (i) processes the output of V(D)J alignment tools, (ii) assigns clonal clusters to Ig sequences and (iii) reconstructs germline sequences. It also offers applications to import data from the frequently used IMGT/HighV-QUEST tool and a set of utilities to perform basic database operations, such as sorting, filtering and modifying annotations.
A universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments.
Assists users with the annotation of genes, clusters sequences, and assembles lineage trees. BRILIA is a B-cell receptors (BCRs) annotation algorithm that refines annotations by exploiting mechanistic biases in somatic hypermutation (SHM) patterns, N region nt compositions, and directionality of N region synthesis by terminal deoxynucleotidyl transferase on the coding versus non-coding DNA strand.
Models antibody somatic hypermutation (SHM) while accounting for sequencing error. ImmuniTree is a Bayesian phylogeny algorithm consisting of an alternative approach to conventional phylogenetic analyses. This software relies on a probabilistic model that describes both the expansion process of a clone and the sequencing process.
Builds lineage trees from an immunoglobulin (Ig) variable region gene sequence alignment. IgTree is an application based on an algorithm which is an extension of the distance method concept. It aims to generate a tree with the minimal number of mutations where every node is separated from its immediate ancestor by only one mutation. The application can also be applied to accommodate gene conversion.
Allows analysis of the complete immune repertoire of different species. ARGalaxy is a web server for analyzes and visualization of T-cell receptor (TCR) and B-Cell Receptor (BCR) sequencing data. It consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. All parts can be run independently or combined, depending on the available data and the question of interest.