Main SLiMSuite short linear motif discovery and analysis tools

• CompariMotif. A unique motif-motif comparison tool for identifying similar SLiMs. Used for clustering results of predictions and identifying known motifs.
• GABLAM. BLAST-based protein similarity scoring and clustering. Used for (Q)SLiMFinder and SLiMProb adjustments for evolutionary relationships.
• GOPHER. Automated orthologue prediction and alignment algorithm. Used for conservation-based masking ((Q)SLiMFinder/SLiMProb) and prediction (SLiMPrints).
• PeptCluster = Peptide alignment, pairwise distance and clustering tool.
• QSLiMFinder. Query-based variant of SLiMFinder with increased sensitivity and specificity, ideal for SLiM discovery from host-pathogen interactions or where at least one interaction is established experimentally.
• SLiMBench = SLiM discovery benchmarking tool.
• SLiMCore = SLiMSuite core module with MegaSLiM and UPC functions for pregenerating (Q)SLiMFinder and SLiMProb data.
• SLiMFarmer. SLiMSuite wrapper for multi-threaded batch processing.
• SLiMFinder. The first de novo SLiM prediction based on a statistical model of over-represented motifs in unrelated proteins. Repeatedly achieves the greatest specificity in benchmarking.
• SLiMList = Short Linear Motif manipulation, filtering and reformatting module.
• SLiMMaker. A simple tool for converting aligned peptides or SLiM occurrences into a regular expression motif.
• SLiMMutant = Short Linear Motif Mutation Analysis Tool. (Development only and currently unsupported.)
• SLiMParser. SLiMSuite wrapper for generating and retrieving SLiMSuite REST server jobs.
• SLiMProb. Unique tool providing biological context (disorder & conservation) for searches of pre-defined SLiMs along with under- and over-representation statistics, correcting for evolutionary relationships. Formerly called SLiMSearch 1.x but renamed to avoid confusion with SLiMSearch2.

Main SeqSuite sequence analysis and genomics tools

SeqSuite: Miscellaneous biological sequence analysis toolkit

SeqSuite is a wrapper for the SeqList tool (libraries/rje_seqlist.py), which includes a number of sequence parsing and formatting functions. The other tools and functions wrapped by SeqSuite are:

• Apollo = GABLAM wrapper for searching against apollo genomes.
• BUSCOMP = BUSCO Compiler and Comparison tool. Used for genome assembly completeness estimates that are robust to sequence quality, and for compiling BUSCO results.
• Diploidocus = Diploid genome assembly analysis toolkit. Includes assembly cleanup (haplotig/artefact removal), genome size prediction and read depth copy number analysis.
• ExTATIC = Developmental only. Extensions and Truncations from Alternative Translation Initiation Codons.
• FIESTA = Fasta Input EST Analysis. Transcriptome annotation/querying. (Not currently supported.)
• GASP = Gapped Ancestral Sequence Prediction. Predicts protein ancestral sequences from a multiple sequence alignment and phylogenetic tree.
• HAQESAC = Homologue Alignment Quality, Establishment of Subfamilies and Ancestor Construction. High throughput generation of high quality mutliple sequence alignments.
• MultiHAQ = Multi-Query HAQESAC controller.
• PAFScaff = Pairwise mApping Format reference-based scaffold anchoring and super-scaffolding. Uses minimap2 to map a genome assembly onto reference chromosomes.
• PAGSAT = Pairwise Assembled Genome Sequence Analysis Tool. Reference-based genome assembly analysis tool. (Development only.)
• PINGU = Protein Interaction Network & GO Utility. (Not currently supported.)
• SAAGA = Summarise, Annotate & Assess Genome Annotations. Uses a reference proteome to summarise and assess genome annotations.
• SAMPhaser = Diploid chromosome phasing from SAMTools Pileup format of mapped long reads.
• Seq = Fasta file sequence manipulation/reformatting tools. Optimised for small sequence datasets.
• SeqList = Updated fasta file sequence manipulation/reformatting tool. Summarise, reformat, and edit large sequence datasets.
• SeqMapper = Sequence Mapping Program.
• SMRTSCAPE = SMRT Subread Coverage & Assembly Parameter Estimator. (Development only)
• Snapper = BLAST-based SNV to feature annotations mapping and rating tool. (Development only)
• Zen - Random Zen wisdom generator and test code.

NB. A number of minor and/or developmental features are not included in this list. Please get in touch if you stumble across anything that looks interesting and want to know more. Collaborations welcome!