The following tools are available for use through the CIPRES REST API. The text in
bold is the tool's ID.
The 'REST Tool Info' links explain how to configure the tools through the REST API.
Since most of these tool's are also available on the CSG, a link to the tool's information page on
the CSG is also provided.
ASTRAL_XSEDE, ASTRAL 5.15.4: Coalescent-based species tree estimation run on XSEDE
BALI_PHY3_XSEDE, Bali-Phy, estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences
BEAST2_XSEDE, BEAST2 v2.6.6: Bayesian Evolutionary Analysis by Sampling Trees
BEAST_TG, BEAST v1.10.4+: Bayesian Evolutionary Analysis by Sampling Trees
BEAST_TG18, BEAST v1.8.4: Bayesian Evolutionary Analysis by Sampling Trees
BLASTN, BLAST-N, using threading on a full node for performance
BWA_XSEDE, BWA: Mapping low-divergent sequences against a large reference genome.
CLANN_EXPANSE, CLANN 4.2.5: Supertree Inference
CLEARCUT, Clearcut v1.0.9: Rapid, relaxed neighbor joining
CLUSTALW, ClustalW v2.1: Create multiple sequence alignments
CONSENSE, Consense v3.66: Calculate consensus trees (Phylip)
CUTADAPT_XSEDE, CUTADAP V 3.4, Remove adapter sequences from high-throughput sequencing reads
DIVVIER_XSEDE, Divvier v1.0: Address MSA uncertainty and error with software run on XSEDE
EPA_NG_XSEDE, EPA NG 0.3.7: Tree inference using evolutionary placement algorithm on XSEDE
EXABAYES_XSEDE, ExaBayes v1.5.1: Tree inference using bayesian on XSEDE
FASTML_XSEDE, FastML v3.1.1: Rapid tree inference using neighbor joining on XSEDE
FASTTREE_XSEDE, FastTree2 v2.1.10: Rapid tree inference using neighbor joining on XSEDE
GARLI2_TGB, GARLI v2.10: Genetic algorithm, maximum likelihood inference for large datasets, run on Teragrid
GARLI_CONF_CREATOR, GARLI.conf Creator: Creates garli.conf files
GATK_XSEDE, A flexible read trimming tool for Illumina NGS data.
GBLOCKS_XSEDE, GBLOCK v0.91b. Selection of conserved blocks from multiple alignments for phylogenetic analysis
GENETREE_XSEDE, GENETREE, v.8.3 Estimation of mutation, migration and growth rates, and ancestral inference
GPHOCS_XSEDE, G-PHOCS v1.3.2 Bayesian inference of ancient human demography from individual genome sequences
GUIDANCE2_XSEDE, Guidance2 v2.0.2 Accurate detection of unreliable alignment regions.
IMA3_XSEDE, IMa3p v.1.11. Efficient phylogenomic software by maximum likelihood, run on XSEDE
IMGC_XSEDE, IMGC v.1.0. Efficient phylogenomic software by maximum likelihood, run on XSEDE
IQTREE_GENEIOUS, IQTree v.2.2.2.7 Efficient phylogenomic software by maximum likelihood, run on XSEDE
IQTREE_XSEDE_1_01_01, IQTREE v.1.6.1, Efficient phylogenomic software by maximum likelihood, run on XSEDE
IQTREE_XSEDE_EXPANSE, IQTree v.2.1.2 Efficient phylogenomic software by maximum likelihood, run on XSEDE
JMODELTEST2_XSEDE, jMODELTEST2 v2.1.6: Statistical selection of best-fit models of nucleotide subtitution
LOGCOMBINER, LOGCOMBINER v1.8.4 - 2.6.3. The LogCombiner utility from the BEAST Package.
MAFFT_TG, MAFFT v7.471: Multiple sequence alignment based on fast Fourier transform on XSEDE
MAFFT_XSEDE, MAFFT v7.505: Multiple sequence alignment based on fast Fourier transform on XSEDE
METASPADES_METAMARC_XSEDE, Metaspades/Metamarc workflow v3.13.0.Metaspades Metamarc workflow: Using HMMs to find Antibiotic Resistance Genes
MIGRATEN_XSEDE, Migrate-N v4.4.4: Estimation of Population Sizes and Gene Flow using the Coalescent
MODELTEST_NG_XSEDE, MODELEST-NG v.0.1.5 Statistical selection of best-fit models of nucleotide and protein subtitution
MPBOOT_XSEDE, Statistical selection of best-fit models of nucleotide and protein subtitution
MRBAYES_RESTART_XSEDE, MrBayes v3.2.7 Restart: Tree inference using Bayesian analysis - run on XSEDE
MRBAYES_XSEDE, MrBayes v3.2.7: Tree inference using Bayesian analysis run on XSEDE
MUSCLE, MUSCLE v3.7: Create multiple alignments from sequences or profiles
MUSCLE_PARALLEL_XSEDE, MUSCLE v5.0: Create multiple alignments from sequences or profiles
NCLCONVERTER, NCLCONVERTER: Interconvert a number of phylogenetic tool formats
NOISY_XSEDE, Noisy v.1.5.12. Identify homo-plastic characters in multiple sequence alignments
PARALLELSTRUCTURE_XSEDE, ParallelStructure v.2.3.4. Population structure using multi-locus genotype data.
PAUPRAT, PAUPrat: PAUP analyses using the Nixon ratchet
PAUP_XSEDE, PAUP v.4.a168 Phylogeneitc Analysis using parsimony.
PHMMER_XSEDE, PHMMER v3.3.2. Biological sequence analysis using profile hidden Markov models
PHYLOBAYES_XSEDE, PhyloBayes: Phylogenetic reconstruction using infinite mixtures
PHYLOBAYES_XSEDE_RESTART, PhyloBayes Restart: Phylogenetic reconstruction using infinite mixtures
PICARD_XSEDE, PICARD v.2.3.0 A tool for manipulating Illumina NGS data.
POY, POY v4.1.2: Iterative sequence alignment and tree inference
PREQUAL_XSEDE, PRE-alignment QUALity appraisal of sequence data.
PROBALIGN, PROBALIGN v1.3: Create multiple alignments from nucleic acid or protein sequences
PROBCONS, PROBCONS v1.12: PROBabilistic CONSistency-based multiple alignment of amino/nucleic acid sequences
PROCESSRADTAGS_XSEDE, ProcessRadTags v1.44 Process Radtags on XSEDE
RAXMLHPC2BB, RAxML v8.1.12 Black Box: Simplified interface for RAxML with rapid bootstrapping run on XSEDE
RAXMLHPC2_TGB, RAxMLHPC v8.1.12: Legacy Interface for Tree inference with rapid bootstrapping run on XSEDE
RAXMLHPC2_WORKFLOW, RAxMLHPC v8.1.12 Workflow: Multistep RAxML workflows on XSEDE
RAXMLHPC8_REST_XSEDE, RAxMLHPC v8.1.24: Tree inference with rapid bootstrapping run on XSEDE
RAXMLNG_XSEDE, RAxMLHPC v.1.0.1: Tree inference with rapid bootstrapping run on XSEDE
READSEQ, READSEQ v2.2: Interconvert a number of sequence formats
SEQBOOT, SEQBOOT v3.66: Bootstrap, jackknife, or permutation resampling (Phylip)
SPADES_ACCESS, SPAdes 3.13.0 for de novo genome assembly
STACKS_XSEDE, Phylogenomics
STATALIGN_ACCESS, STATALIGN v3.4: Bayesian Tree Inference using both Substitution and Indel information
TREEANNOTATOR, TREEANNOTATOR v.1.8.4-2.6.3. The TreeAnnotator utility from the BEAST Package.
TRIMAL_XSEDE, TRIMAL v.1.2.59 Trim sequence alignments.
TRIMMOMATIC_XSEDE, Trimmomatic v.0.36 A flexible read trimming tool for Illumina NGS data.
