Phylogeny / Alignment Tools

  • ASTRAL on XSEDE (5.15.4) - Coalescent-based species tree estimation
  • BAli-Phy on XSEDE (3.4.1-3.5.0) - BAli-Phy estimates multiple sequence alignments and evolutionary trees.
  • BEAST2 on XSEDE (2.1 - 2.6.3) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • BEAST (current) on XSEDE (1.10.4/1.10.5pre) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • BEAST (old) on XSEDE (1.8.4) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • Clearcut (1.0.9) - Fast Implementation of Relaxed Neighbor Joining
  • ClustalW (2.1) - Create Multiple Alignments from Sequences
  • Consense (Phylip 3.66) - Find A Consensus Tree
  • Cutadapt on XSEDE (3.4) - Remove adapter sequences from high-throughput sequencing reads
  • DPPDIV on XSEDE (1.0) - Estimating species divergence times and lineage-specific substitution rates on a fixed topology run on XSEDE
  • EPA-NG on XSEDE (0.3.7) - Massively Parallel Evolutionary Placement of Genetic Sequences - run on XSEDE
  • ExaBayes on XSEDE (1.5.1) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • FastML on XSEDE (3.1) - Fast (Approximate) Maximum Likelihood tree construction - run on XSEDE
  • FastTreeMP on XSEDE (2.1.10) - Fast (Approximate) Maximum Likelihood tree construction - run on XSEDE
  • GARLI 2.10 on XSEDE (2.10) - Genetic Algorithm for Rapid Likelihood Inference - run on XSEDE.
  • GARLI.conf Creator (2.0) - Creates a Garli.conf file for up to five partitions
  • GBLOCKS on XSEDE (0.91b) - Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis - run on XSEDE
  • G-PhoCS on XSEDE (1.3.2) - A Generalized Phylogenetic Coalescent Sampler
  • Guidance2 on XSEDE (2.02) - Accurate detection of unreliable alignment regions - run on XSEDE.
  • IMa3 on XSEDE (1.11) - IMa3p - Parallel MCMC and inference of ancient demography under the Isolation with Migration (IM) model
  • IQ-Tree on XSEDE (2.1.2) - Efficient phylogenomic software by maximum likelihood, run on XSEDE
  • jModelTest2 on XSEDE (2.1.6) - Statistical selection of best-fit models of nucleotide substitution, run on XSEDE
  • LogCombiner on XSEDE (1.8.4-2.6.0) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • MAFFT on XSEDE (7.471) - Multiple alignment program for amino acid or nucleotide sequences; parallel version
  • MetaSpades/MetaMarc Workflow on XSEDE (3.13.0) - Metaspades Markov Model Search for antibiotic resistance genes in environmental samples
  • Migrate-N on XSEDE (4.4.4) - Estimation of Population Sizes and Gene Flow using the Coalescent
  • ModelTest-NG on XSEDE (0.1.5) - Statistical selection of best-fit models of nucleotide and protein substitution, run on XSEDE
  • MrBayes Restart on XSEDE (3.2.x) - Tree Inference Using Bayesian Analysis - run on XSEDE
  • MrBayes on XSEDE (3.2.7a) - Tree Inference Using Bayesian Analysis - run on XSEDE
  • Muscle (3.7) - Create Multiple Alignments from Sequences or Profiles
  • NCLconverter (2.1) - A file format transformation tool
  • Noisy on XSEDE (1.5.12) - Identify homo-plastic characters in multiple sequence alignments - run on XSEDE
  • ParallelStructure on XSEDE (2.3.4) - A program to investigate population structure using multi-locus genotype data
  • PartitionFinder2 on XSEDE (2.1.1) - Selecting best-fit partitioning schemes and models of evolution
  • PAUPRat (Not specified) - Parsimony ratchet searches using PAUP*
  • PAUP on XSEDE (4.a168) - Phylogenetic Analyses Using Parsimony*
  • Phylobayes MPI on XSEDE (1.8c) - Phylogenetic reconstruction using infinite mixtures - run on XSEDE
  • Phylobayes MPI on XSEDE (Restart) (1.8c) - Restart a PhyloBayes MPI run on XSEDE
  • POY (4.1.2) - Phylogenetic tree inference using dynamic homologies.
  • Probalign (1.3) - Multiple sequence alignment using partition function posterior probabilities.
  • ProbCons (1.12) - Probabilistic Consistency-based Multiple Alignment of Amino/Nucleic Acid Sequences
  • RAxML-HPC BlackBox (8.2.12) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping on XSEDE.
  • RAxML-HPC2 on XSEDE (8.2.12) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping run on XSEDE
  • RAxML-HPC2 Workflow on XSEDE (8.2.12) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping run on XSEDE
  • RAxML-HPC v.8 on XSEDE (8.2.12) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping run on XSEDE
  • RAxML-NG (1.0.1) - RAxML-NG offers improvements in speed, flexibility and user-friendliness over previous RAxML versions.
  • Readseq (2.2) - Readseq: biological sequence format interconversion utility
  • Seqboot (Phylip 3.66) - Bootstrap, Jackknife, or Permutation Resampling
  • TreeAnnotator on XSEDE (1.8.4-2.6.0) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • TrimAl on XSEDE (1.2.59) - Trim alignments using TrimAl - run on XSEDE