Tree-Based Alignment Selector Toolkit
Create patristic distance rings with DendroPy
Align sequences with MAFFT
Maximum likelihood tree inference
Fast maximum likelihood tree inference
Bayesian phylogenetic tree inference
Reconstruct tree from microsatellite data
Multispecies coalescent from gene trees and PhyParts to show gene tree conflict
Show multiple node support values on tree using Mesquite Hypha
Create networks using TCS or upload graph file
Infer splits phylogenetic networks using Neighbor-Net
Create haplotype table with MeShClust
Cluster sequences with QIIME (UCLUST) or VSEARCH
Import csv file to graph
NGMLST: Next Generation Multilocus Sequence Typing using DADA2
DADA2: Infer exact amplicon sequence variants (ASVs) from barcode sequences
Process data for structure tool
Use phyloseq object to create graphs
Select fungal taxonomy using UNITE or NCBI ITS database
Download FASTA and metadata for query of GenBank
Split combined ITS/LSU into separate files with ITSx
Create taxonomy csv file from list of scientific names
View T-BAS results from database for a run ID
View T-BAS results from database for specimens
Download tree NEXUS files from treebase database
Search in GNPS spectral libraries for metabolite
Place MASST search results on NCBI taxonomy tree
Update T-BAS metadata with genus, species taxids.
Concatenate several loci or generate single locus files
Merge two voucher tables into one
Extend alignment with additional sequence
Append several text files into one file
Get set results from lists in 2 files
Convert Phylogenetic tree from Newick to Nexus format
Convert sequence file(s) to different format with sites variable report
Create new FASTA files using a strain list
Extract chromosome FASTA files from a Map file
Create protein and DNA locus files from annotations using phmmer and nhmmer output, respectively
Sort FASTA file by lengths
Rename FASTA headers with filename and append
Install locally and run neutrality test
Estimation of migration rates using Isolation-with-Migration (IMa3) models
Show tree with structure plots
IMgc on CIPRES
Fast Phage Annotation Tool
Prophage Estimation Tool
Tools for population genetics and multi‑omics analysis
Popgen Pipeline Platform (PPP) for population genomic analyses
ViralSeq pipeline for NGS analysis of cassava mosaic begomoviruses
Create pie charts
Upload archive created by TBAS or DeCIFR utility
Collapse low support nodes on tree
View telescope tree from MEP file
Retrieve MEP files from archive by run ID
Retrieve names from tree or sequence file
Update names in tree or sequence file with replacements from csv
Create taxonomy CSV file from taxon string
Create FASTA locus files from genome annotations
Get CIPRES XML from jobs URL
Show jobs submitted to CIPRES (admin)
Show jobs submitted to CIPRES (user)
Add new accessions to JSON config file for T-BAS guide tree
Big Tree Viewer
Unzip MEP file for REST
Retrieve submitted tree, alignments, and metadata from archive by accession ID
Merge columns in T-BAS metadata
Convolutional neural networks to predict host phenotype from metagenomic data
This pipeline extracts and filters Rhs-toxins from GenBank files, creating a summary of Rhs sequences for each genome.
Copyright © 2014, CENTER FOR INTEGRATED FUNGAL RESEARCH. All Rights Reserved.