DeCIFR

T-BAS Toolkit

Tree-Based Alignment Selector Toolkit

Patristic Distance

Create patristic distance rings with DendroPy

MAFFT

Align sequences with MAFFT

RAxML and FastTree

Maximum likelihood tree inference

IQ-TREE

Fast maximum likelihood tree inference

BEAST

Bayesian phylogenetic tree inference

Microsatellite tree

Reconstruct tree from microsatellite data

ASTRAL

Multispecies coalescent from gene trees and PhyParts to show gene tree conflict

EPA-ng

Fast, parallel, highly accurate Maximum Likelihood Phylogenetic Placement

Graph Inference

Create networks using TCS or upload graph file

SplitsTree

Infer splits phylogenetic networks using Neighbor-Net

Mesquite Hypha

Show multiple node support values on tree using Mesquite Hypha

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

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

GNPS Library Search

Search in GNPS spectral libraries for metabolite

GNPS Ontology

Place MASST search results on NCBI taxonomy tree

GenBank IDs

Update T-BAS metadata with genus, species taxids.

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

Rename FASTA headers

Rename FASTA headers with filename and append

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

Pharokka

Fast Phage Annotation Tool

ProphET

Prophage Estimation Tool

Galaxy

Tools for population genetics and multi‑omics analysis

Galaxy - PPP

Popgen Pipeline Platform (PPP) for population genomic analyses

Galaxy - Cassava Virus Evolution

ViralSeq pipeline for NGS analysis of cassava mosaic begomoviruses

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 Tool

Add new accessions to JSON config file for T-BAS guide tree

D3 SVG and Canvas

Big Tree Viewer

REST

Unzip MEP file for REST

T-BAS accession

Retrieve submitted tree, alignments, and metadata from archive by accession ID

Merge Metadata

Merge columns in T-BAS metadata

PopPhy-CNN

Convolutional neural networks to predict host phenotype from metagenomic data

Rhs-toxin Extraction Pipeline

This pipeline extracts and filters Rhs-toxins from GenBank files, creating a summary of Rhs sequences for each genome.

MiMeNet

Exploring microbiome-metabolome relationships using neural networks

MiMeNet postprocessing

Exploring microbiome-metabolome relationships using neural networks

PECAT