Phylogenetic and network methods
T-BAS Toolkit
Tree-Based Alignment Selector Toolkit
Patristic Distance
Create patristic distance rings with DendroPy
MAFFT
Align sequences with MAFFT
Tree Inference
Run de novo tree inference using RAxML
Graph Inference
Create networks using TCS or upload graph file
Mesquite Hypha
Show multiple node support values on tree using Mesquite Hypha
SplitsTree
Infer splits phylogenetic networks using Neighbor-Net
Metabarcoding methods
MeShClust
Create haplotype table with MeShClust
Cluster Sequences
Cluster sequences with QIIME (UCLUST) or VSEARCH
Graph CSV
Import csv file to graph
NGMLST
NGMLST: Next Generation Multilocus Sequence Typing using DADA2
DADA2
DADA2: Infer exact amplicon sequence variants (ASVs) from barcode sequences
Structure Files
Process data for structure tool
Phyloseq
Use phyloseq object to create graphs
Database search methods
BLAST Taxonomy
Select fungal taxonomy using UNITE or NCBI ITS database
Query GenBank
Download FASTA and metadata for query of GenBank
ITSx
Split combined ITS/LSU into separate files with ITSx
Create Taxonomy
Create taxonomy csv file from list of scientific names
T-BAS Results Database
View T-BAS results from database for a run ID
T-BAS Specimen Database
View T-BAS results from database for specimens
Treebase
Download tree NEXUS files from treebase database
File manipulation and conversion
Concatenate Loci
Concatenate several loci or generate single locus files
Merge Vouchers
Merge two voucher tables into one
Extend Sequence
Extend alignment with additional sequence
Append Files
Append several text files into one file
Get Set Results
Get set results from lists in 2 files
Nwk2nexus
Convert Phylogenetic tree from Newick to Nexus format
Sequence Converter
Convert sequence file(s) to different format with sites variable report
FASTA from list
Create new FASTA files using a strain list
Extract Chromosome FASTA
Extract chromosome FASTA files from a Map file
Loci from Annotations
Create protein and DNA locus files from annotations using phmmer and nhmmer output, respectively
Sort FASTA
Sort FASTA file by lengths
Population genetic methods
Neutrality
Install locally and run neutrality test
IMa3
Estimation of migration rates using Isolation-with-Migration (IMa3) models
Structure
Show tree with structure plots
IMgc
IMgc on CIPRES
Galaxy@NCSTATE
Galaxy
Tools for population genetics and multi‑omics analysis
Utilities
Piechart
Create pie charts
Archive
Upload archive created by TBAS or DeCIFR utility
Collapse Tree
Collapse low support nodes on tree
Telescope Viewer
View telescope tree from MEP file
MEP Archive
Retrieve MEP files from archive by run ID
Retrieve Names
Retrieve names from tree or sequence file
Update Names
Update names in tree or sequence file with replacements from csv
Extract Taxonomy
Create taxonomy CSV file from taxon string
Filter FASTA
Create FASTA locus files from genome annotations
CIPRES Jobs
Get CIPRES XML from jobs URL
CIPRES Jobs Database
Show jobs submitted to CIPRES (admin)
CIPRES Jobs Database User
Show jobs submitted to CIPRES (user)
guide_tree_edit
Add to json config for Guide tree
D3 SVG and Canvas
Big Tree Viewer
