Installed This software should be available with no extra configuration. muscle-5.1.0 MUSCLE is widely-used software for making multiple alignments of biological sequences. Version 5 of MUSCLE achieves highest scores on Balibase, Bralibase and Balifam benchmark tests and scales to thousands of sequences on a commodity desktop computer. This version supports generating an ensemble of alternative alignments with the same high accuracy obtained with default parameters. By comparing downstream predictions from different alignments, such as trees, a biologist can evaluation the robustness of conclusions against alignment errors.

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-1.1.1 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. primer3-2.6.1 Primer3 picks primers for PCR reactions, considering as criteria: oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities, PCR product size, positional constraints within the source (template) sequence, and possibilities for ectopic priming (amplifying the wrong sequence) many other constraints. All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair.

Installed This software should be available with no extra configuration. bppsuite This is the final release of the software before the official bppsuite 3.0.0 release. Examples Example code can be found here: 1 /local/downloads/bppsuite-rel299/Examples PDF Manual Download the bppsuite pdf manual here Location 1 2 $ which bppml /local/cluster/bin/bppml help message 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 $ bppml ****************************************************************** * Bio++ Maximum Likelihood Computation, version 2.

Configuration required See the relevant section below to configure this software before use. EnTAP-0.10.8 EnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates, while focusing primarily on protein-coding transcripts. Following filters applied through assessment of true expression and frame selection, open-source tools are leveraged to functionally annotate the translated proteins.

Conda See the ‘activating the conda environment’ section below to access this software. Configuration required See the relevant section below to configure this software before use. busco-5.4.3 - Benchmarking sets of Universal Single-Copy Orthologs. For full documentation please consult the user guide: https://busco.ezlab.org/busco_userguide.html Main changes in v5: Metaeuk is used as default gene predictor for eukaryote pipeline. Augustus is maintained and can be used optionally instead of Metaeuk.