The following bioinformatics software tools are hosted by ELIXIR Ireland associated researchers:

Tool Description
RiboGalaxy An instant of Galaxy tailored for ribosome profiling data analysis.
Maintainer: Pavel Baranov
PAUSEPRED A very simple applet for predicting ribosome pauses using ribosome profiling data. Not great, but better than nothing and nothing else is available for this purpose, hence the tool remains popular.
Maintainer: Pavel Baranov
Trips-viz A computational environment for the analysis and visualisation of public and user-generated ribosome profiling data mapped to transcriptomes.
Maintainer: Pavel Baranov
BRCA-Core Source code (Python) to identify protein complexes co-regulated in tumour proteomic samples.
Maintainer: Colm Ryan
Homo (v2.1) Source code (C++). A program for analysing compositional heterogeneity across aligned sequence data (controls the family-wise error rate and the false discovery rate). The software also computes three compositional distances and the p distance.
Maintainer: Lars Jermiin
SatuRation (v1.0) Source code (C++). A program designed to estimate the degree of saturation observed between two sequences of nucleotides, genotypes, di-nucleotides, codons or amino acids.
Maintainer: Lars Jermiin
AliStat (1.14) Source code (C++). Software for quantifying the completeness of multiple sequence alignments used in phylogenetic and phylogenomic research.
Maintainers: Thomas Wong , Lars Jermiin
HAL-HAS (v2.6.4) Source code (C++). Software for identifying optimal models of sequences evolution, which uses mixture models nucleotide sequence evolution that account for rate heterogeneity across sites and across lineages.
Maintainer: Thomas Wong
Hetero2 (v2.4) Source code (C++). Software to simulate the evolution of nucleotide sequences on phylogenetic trees under heterogeneous Markovian conditions.
Maintainers: Thomas Wong
AliJack (v1.0) Source code (C++). Software to randomly sample subsets of sequences from a multiple sequence alignment. The jackknife procedure is used.
Maintainer: Thomas Wong
CheckJack (v1.0) Source code (C++). Software to compute jackknife scores from trees generated from alignments generated using AliJack.
Maintainer: Thomas Wong
ModelFinder (v1.0) Source code (C++). Software for model selection during phylogenetic analysis of nucleotide and amino acid sequences. ModelFinder is embedded in UQ-TREE and IQ-TREE 2 and can only be access by downloading these programs.
Maintainers: Minh Bui , Thomas Wong , Lars Jermiin
NMF An R package for non-negative matrix factorization.
Maintainer: Cathal Seoighe
CellMix An R package for gene expression deconvolution.
Maintainer: Cathal Seoighe
LymAnalyzer A java tool for profiling short-read sequences from T cell receptors and immunoglobulins.
Maintainer: Cathal Seoighe
SLiMs A comprehensive suite of tools and repositories for the analysis, visualisation and dissemination of the short functional modules, known as short linear motifs or SLiMs, with training available.
Maintainer: Denis Shields
Clustal Omega Multiple Sequence Alignment package via on-line server, in collaboration with groups in Germany, the UK and France.