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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

Protein Analysis

Data Management