Cipres Web Portal

Tools

  • Boxshade (3.31) - Pretty printing of aligned PS or DS
  • Clearcut (1.0.9) - Fast Implementation of Relaxed Neighbor Joining
  • ClustalW (1.82) - Create Multiple Alignments from Sequences
  • Consense (Phylip 3.66) - Find A Consensus Tree
  • CONTRAlign (2.01) - CONditional TRAining for Sequence Alignment
  • Drawgram (Phylip 3.66) - Plots a cladogram- or phenogram- rooted tree
  • Drawtree (Phylip 3.66) - Plots an unrooted tree diagram
  • Format Validator (1.0) - Format Validation Tool
  • FSA (1.15.0) - Distance-based alignment of DNA, RNA and proteins.
  • GARLI on Lonestar (0.960) - Genetic Algorithm for Rapid Likelihood Inference - run on teragrid.
  • MAFFT (6.240) - Multiple alignment program for amino acid or nucleotide sequences
  • MrBayes on Abe (3.1.2) - Tree Inference Using Bayesian Analysis - run on teragrid
  • Muscle (3.7) - Create Multiple Alignments from Sequences or Profiles
  • MView_Alig (1.41.10) - Multiple Alignment Viewer
  • NCLconverter (2.1) - A file format transformation tool
  • PAUP (4.0b10) - CIPRES wrapper around PAUPs HSearch command (using parsimony).
  • POY (4.1.2) - Phylogenetic tree inference using dynamic homologies.
  • Probalign (1.2) - Multiple sequence alignment using partition function posterior probabilities.
  • ProbCons (1.12) - Probabilistic Consistency-based Multiple Alignment of Amino/Nucleic Acid Sequences
  • RAxML-HPC BlackBox (7.2.6) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping on teragrid.
  • RAxML-HPC2 on Abe (7.2.6) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping (beta interface) run on teragrid.
  • Readseq (2.2) - Readseq: biological sequence format interconversion utility
  • RID3Paup (r5011) - Recursive-Iterative-DCM3 algorithm with Paup parsimony search.
  • RID3Raxml (r5011) - Recursive-Iterative-DCM3 algorithm with RaxmlHPC search.
  • Seqboot (Phylip 3.66) - Bootstrap, Jackknife, or Permutation Resampling

  • If there is a tool or a feature you need, you can add it yourself or let us know.

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