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리소스

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Phylogenetics

  • GARLI Fast maximum likelihood tree building on large datasets with GARLI
  • 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
  • DualBrothers Identify recombination events in phylogenetic history with DualBrothers
  • Species Delimitation Assess putative species in phylogenetic trees

Nucleotide 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
  • CRT Find existing CRISPR sites in bacteria and archaea
  • EMBOSS Nucleotide 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

Protein Analysis

Services and Searching

  • Biocode LIMS Integrated laboratory information management system for DNA barcoding
  • EuPathDB Search and download eukaryotic pathogen genes
  • Find Big Folders List the size of all folders in your local database
  • GenBank Submission Simplified submission of sequences, genomes, features, primers and traces.
  • Go To Documents Jump to documents by entering their unique IDs
  • Groovy Console Opens a terminal window inside Geneious for scripting in the Groovy language
  • Sequence Classifier Taxonomically classify samples against your own database of known sequences

Alignment

  • 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

Assembly

  • 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
  • Contig Sorter
  • FLASH Merge paired sequencing reads using FLASH
  • MIRA Efficient and accurate sequence assembly with MIRA
  • Tophat Fast splice junction mapping for RNA-Seq reads with TopHat
  • Velvet De novo assembly of short reads with Velvet