Software
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.
Maintainer: |