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
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
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
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.
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
Rename FASTA headers
Rename FASTA headers with filename and append
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
Pharokka
Fast Phage Annotation Tool
ProphET
Prophage Estimation Tool
Galaxy@CIFR
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
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 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
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