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 (2.6.6) - 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
  • BlastN (2.2.1) - Search DBs for Nucleotide Sequence similarity
  • BWA on XSEDE (0.36) - Burrows-Wheeler Alignment Tool. (Make sure no white space exists in any of the alphabet input fields on this page. This does not apply to Enter your data below field.)
  • 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
  • DEPP on XSEDE (unk) - Sequence aligment by deep learning - run on XSEDE
  • Divvier on XSEDE (1.01) - Address MSA uncertainty and error with software 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 (3.1.1) - 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
  • GATK on XSEDE (3.5) - Variant Discovery in High-Throughput Sequencing Data
  • GBLOCKS on XSEDE (0.91b) - Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis - run on XSEDE
  • Genetree on XSEDE (8.3) - Estimation of mutation, migration and growth rates, and ancestral inference
  • 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
  • IMgc on XSEDE (1.0) - Extract optimal recombination-filtered blocks (no four-gamete violations) from recombination-rich genomic re-sequence data
  • 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 (7.490) - Multiple alignment program for amino acid or nucleotide sequences; parallel version
  • 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 (4.4.4-5.0.4) - 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
  • MPboot on XSEDE (1.1.0) - Fast maximum parsimony tree inference - 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
  • Muscle Parallel (5.0) - 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
  • PAUPRat (Not specified) - Parsimony ratchet searches using PAUP*
  • PAUP on XSEDE (4.a168) - Phylogenetic Analyses Using Parsimony*
  • PHMMER on XSEDE (3.3.2) - Biological sequence analysis using profile hidden Markov models - run on XSEDE
  • 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
  • PICARD on XSEDE (2.3.0) - Tools for manipulating high-throughput sequencing (HTS) data and formats
  • POY (4.1.2) - Phylogenetic tree inference using dynamic homologies.
  • PREQUAL on XSEDE (1.02) - PRE-alignment QUALity assessment on XSEDE
  • Probalign (1.3) - Multiple sequence alignment using partition function posterior probabilities.
  • ProbCons (1.12) - Probabilistic Consistency-based Multiple Alignment of Amino/Nucleic Acid Sequences
  • Ranger DTL on XSEDE (2.0) - Phylogenetic tree-based annotation of proteins
  • RAxML-HPC BlackBox (8.2.12) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping on XSEDE.
  • 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 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-HPC v.8 on XSEDE, TEST (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 (1.1.0) - RAxML-NG offers improvements in speed, flexibility and user-friendliness over previous RAxML versions.
  • RAxML-NG RESTTEST (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
  • RevBayes on XSEDE (1.1.1) - Tree Inference Using Bayesian Analysis - run on XSEDE
  • 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
  • Tree Grafter on XSEDE (1) - Phylogenetic tree-based annotation of proteins
  • TrimAl on XSEDE (1.2.59) - Trim alignments using TrimAl - run on XSEDE
  • Trimmomatic on XSEDE (0.36) - A flexible read trimming tool for Illumina NGS data
  • UPP on XSEDE (4.5.1) - Ultra-large alignments using Phylogeny-aware Profiles run on XSEDE