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Alignment and Assembly
- Clustal Omega Multiple sequence alignment using the latest addition to the Clustal family.
- LASTZ Align large genomes using LASTZ
- MAFFT Fast and accurate multiple sequence alignment with MAFFT
- Mauve Align multiple genomes to identify large-scale evolutionary events using Mauve
- SeqPartitioner Partition allele multisets from multiple alignments
- BBDuk Adapter/Quality Trimming and Filtering
- BBMap Fast and sensitive aligner for RNA and DNA
- Bowtie Reference mapping with Bowtie
- Cap3 Perform contig assembly using CAP3
- Flye A de novo assembler for single molecule sequencing reads, such as PacBio and Oxford Nanopore
- Minimap2 A versatile mapper / pairwise aligner for genomic and spliced nucleotide sequences
- MIRA Efficient and accurate sequence assembly with MIRA
- Velvet De novo assembly of short reads with Velvet
Phylogenetics
- RAxML Fast maximum-likelihood tree building on large datasets with RAxML
- FastTree Fast phylogenetic tree building of huge datasets
- MrBayes Bayesian phylogenetic analysis using MrBayes
- PAUP* Phylogenetic inference using PAUP* 4.0
- PhyML Phylogenetic inference for molecular evolution using PhyML
- Species Delimitation Assess putative species in phylogenetic trees
Sequence Analysis
- Augustus Eukaryotic gene prediction with Augustus
- Complement/Reverse Complement or Reverse DNA sequences without doing both
- CpG Islands Find targets for DNA methylation by predicting CpG islands
- EMBOSS Mutate and Shuffle Automatically mutate or shuffle sequences
- EMBOSS Nucleotide Analysis Predict transcription factors and protein coding regions
- FreeBayes Haplotype based variant finding with FreeBayes.
- Glimmer Prediction Predict genes in microbial DNA with Glimmer
- Heterozygotes Identify heterozygotes in chromatograms with secondary peak calling
- Microsatellites Streamlined microsatellite genotyping
- Mutate and Shuffle Automatically mutate or shuffle sequences
- Phobos Search genomes for tandem repeats / microsatellites using Phobos
- Polymorphic SSRs Find polymorphic tandem repeats in alignments using Phobos
- Repeat Finder Find large, distant repeats
- Sequence Classifier Taxonomically classify samples against your own database of known sequences
Protein Analysis
- Coiled Coils Predict protein coiled coil regions
- EMBOSS Protein Analysis Predict secondary structure, antigenic regions and signal cleavage sites.
- InterProScan Automatically annotate proteins with InterPro domains
- PDB Structure Aligner Structural alignment of PDB protein sequences
- Transmembrane Prediction Predict transmembrane spanning regions of proteins
Data Management
- Biocode LIMS Integrated laboratory information management system for DNA barcoding
- Dotmatics Platform Integration Enables integration with Dotmatics Bioregister
- GenBank Submission Simplified submission of sequences, genomes, features, primers and traces.