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
- 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
- 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
- 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 (7.490) - 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
- 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*
- 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
- 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
- TrimAl on XSEDE (1.2.59) - Trim alignments using TrimAl - run on XSEDE