Configuration required See the relevant section below to configure this software before use. R-4.2.2 See the latest news here. R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. Link to R FAQ from the r-project To activate this version of R Edit your $PATH to include /local/cluster/R-4.2.2/bin. Make a new directory for your $R_LIBS and set your $R_LIBS to that directory.

Installed This software should be available with no extra configuration. graphtyper-2.7.5 graphtyper is a graph-based variant caller capable of genotyping population-scale short read data sets. It represents a reference genome and known variants of a genomic region using an acyclic graph structure (a “pangenome reference”), which high-throughput sequence reads are re-aligned to for the purpose of discovering and genotyping SNPs, small indels, and structural variants. Usage The recommended way of genotyping small variants (SNP+indels) is using the genotype subcommand

Installed This software should be available with no extra configuration. This software is accessible with an alias. Typing the full path might be required in some situations. anchorwave-1.0.1 AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals. By performing sensitive sequence alignment for each shorter interval via a 2-piece affine gap cost strategy and merging them together, AnchorWave generates a whole-genome alignment for each collinear block.

Installed This software should be available with no extra configuration. metabat2-20221104 It is exciting that MetaBAT has gained some popularity for the last couple of years. One of design goals of original MetaBAT was to enable users to explore MetaBAT parameters efficiently so that they could find the best results out of their dataset. However, the task might have been challenging due to various reasons (e.g. too many parameters to optimize, lack of knowledge about parameters, lack of computing or time resources, etc.

Installed This software should be available with no extra configuration. NGSEP - Next Generation Sequencing Experience Platform Version 4.2.1 (28-06-2022) NGSEP provides an object model to enable different kinds of analysis of DNA high throughput sequencing (HTS) data. The classic use of NGSEP is a reference guided construction and downstream analysis of large datasets of genomic variation. NGSEP performs accurate detection and genotyping of Single Nucleotide Variants (SNVs), small and large indels, short tandem repeats (STRs), inversions, and Copy Number Variants (CNVs).

Installed This software should be available with no extra configuration. Dsuite-20221019 Publication: Malinsky, M., Matschiner, M. and Svardal, H. (2021) Dsuite ‐ fast D‐statistics and related admixture evidence from VCF files. Molecular Ecology Resources 21, 584–595. doi: https://doi.org/10.1111/1755-0998.13265 Free to view author link Malawi cichlid data used in the manuscript: VCF file; SETS.txt file Simulated 20-species data used in the manuscript: VCF file; SETS.txt file; TREE_FILE.nwk (input tree)