Phylogeny / Alignment Tools

If there is a tool or a feature you need, please let us know.
  • APPLES on XSEDE (2.0.11) - Accurate Phylogenetic Placement using LEast Squares (Distance based)
  • ASTRAL-Pro2 on ACCESS (1.15) - Species tree reconstruction
  • ASTRAL on ACCESS (5.15.4) - Coalescent-based species tree estimation
  • BAli-Phy on ACCESS (3.6.1) - BAli-Phy estimates multiple sequence alignments and evolutionary trees.
  • BEAST2 on ACCESS (2.7.6) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • BEAST (current) on ACCESS (1.10.4/1.10.5pre) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • BEAST (old) on ACCESS (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.
  • CLANN (4.2.5) - Software for inferring phylogenetic supertrees
  • 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 ACCESS (3.4) - Remove adapter sequences from high-throughput sequencing reads
  • DEPP on ACCESS (unk) - Sequence aligment by deep learning - run on XSEDE
  • Divvier on ACCESS (1.01) - Address MSA uncertainty and error with software run on XSEDE
  • EPA-NG on ACCESS (0.3.8) - Massively Parallel Evolutionary Placement of Genetic Sequences - run on XSEDE
  • ExaBayes on ACCESS (1.5.1) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • FastML on ACCESS (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 ACCESS (3.5) - Variant Discovery in High-Throughput Sequencing Data
  • GBLOCKS on ACCESS (0.91b) - Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis - run on XSEDE
  • GeneMark on ACCESS (4.371) - Novel eukaryotic genomes can be analyzed by the self-training GeneMark-ES.
  • Genetree on ACCESS (8.3) - Estimation of mutation, migration and growth rates, and ancestral inference
  • G-PhoCS on ACCESS (1.3.2) - A Generalized Phylogenetic Coalescent Sampler
  • Guidance2 on ACCESS (2.02) - Accurate detection of unreliable alignment regions - run on XSEDE.
  • IMa3 on ACCESS (1.11) - IMa3p - Parallel MCMC and inference of ancient demography under the Isolation with Migration (IM) model
  • IMgc on ACCESS (1.0) - Extract optimal recombination-filtered blocks (no four-gamete violations) from recombination-rich genomic re-sequence data
  • IQ-Tree on ACCESS (2.2.2.7) - Efficient phylogenomic software by maximum likelihood, run on XSEDE
  • jModelTest2 on ACCESS (2.1.6) - Statistical selection of best-fit models of nucleotide substitution, run on XSEDE
  • LogCombiner on ACCESS (1.8.4-2.6.0) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • MAFFT on ACCESS (7.505) - Multiple alignment program for amino acid or nucleotide sequences; parallel version
  • MAFFT on ACCESS (7.471) - Multiple alignment program for amino acid or nucleotide sequences; parallel version
  • MetaSpades/MetaMarc Workflow on ACCESS (3.13.0) - Metaspades Markov Model Search for antibiotic resistance genes in environmental samples
  • Migrate-N on ACCESS (4.4.4-5.0.4) - Estimation of Population Sizes and Gene Flow using the Coalescent
  • ModelTest-NG on ACCESS (0.1.7) - Statistical selection of best-fit models of nucleotide and protein substitution, run on XSEDE
  • MPboot on ACCESS (1.2) - Fast maximum parsimony tree inference - run on XSEDE
  • MrBayes Restart on ACCESS (3.2.x) - Tree Inference Using Bayesian Analysis - run on XSEDE
  • MrBayes on ACCESS (3.2.7a) - Tree Inference Using Bayesian Analysis - run on XSEDE
  • Muscle (3.7) - Create Multiple Alignments from Sequences or Profiles
  • Muscle Parallel on ACCESS (5.0) - Create Multiple Alignments from Sequences or Profiles
  • NCLconverter (2.1) - A file format transformation tool
  • Noisy on ACCESS (1.5.12) - Identify homo-plastic characters in multiple sequence alignments - run on XSEDE
  • ParallelStructure on ACCESS (2.3.4) - A program to investigate population structure using multi-locus genotype data
  • PAUPRat (Not specified) - Parsimony ratchet searches using PAUP*
  • PAUPRAT_EXPANSE -
  • PAUP on ACCESS (4.a168) - Phylogenetic Analyses Using Parsimony*
  • PHMMER on ACCESS (3.3.2) - Biological sequence analysis using profile hidden Markov models - run on XSEDE
  • Phylobayes MPI on ACCESS (1.8c) - Phylogenetic reconstruction using infinite mixtures - run on XSEDE
  • Phylobayes MPI on ACCESS (Restart) (1.8c) - Restart a PhyloBayes MPI run on XSEDE
  • PICARD on XSEDE (2.2.8) - Tools for manipulating high-throughput sequencing (HTS) data and formats
  • POY on ACCESS (5.x) - Phylogenetic tree inference using dynamic homologies.
  • PREQUAL on ACCESS (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
  • ProtHint on ACCESS (2.6.0) - Prothint pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome
  • PYTHIA on ACCESS (1.10) - A lightweight python library to predict the difficulty of Multiple Sequence Alignments
  • Ranger DTL on ACCESS (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-HPC2 on ACCESS (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 ACCESS (8.2.12) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping run on XSEDE
  • RAxML-NG on ACCESS (1.2.0) - 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 ACCESS (1.2.1) - Tree Inference Using Bayesian Analysis - run on XSEDE
  • Seqboot (Phylip 3.66) - Bootstrap, Jackknife, or Permutation Resampling
  • SPAdes on ACCESS (3.15.5) - SPAdes for de novo assembly
  • StatAlign (3.4) - Bayesian Tree Inference using both Substitution and Indel information
  • TreeAnnotator on ACCESS (1.8.4-2.6.6) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
  • TrimAl on ACCESS (1.2.59) - Trim alignments using TrimAl - run on XSEDE
  • Trimmomatic on ACCESS (0.36) - A flexible read trimming tool for Illumina NGS data
  • UPP on ACCESS (4.5.1) - Ultra-large alignments using Phylogeny-aware Profiles run on XSEDE