Phylogenetic and network methods

patristic distance
T-BAS Toolkit

Tree-Based Alignment Selector Toolkit

patristic distance
Patristic Distance

Create patristic distance rings with DendroPy

MAFFT tool
MAFFT

Align sequences with MAFFT

denovo
Tree Inference

Run de novo tree inference using RAxML

tcs graph
Graph Inference

Create networks using SplitsTree, TCS or upload graph file

trees 2 hypha tool
Mesquite Hypha

Show multiple node support values on tree using Mesquite Hypha

splitstree
splitstree

computing phylogenetic networks


Metabarcoding methods

meshclust
MeShClust

Create haplotype table with MeShClust

cluster
Cluster Sequences

Cluster sequences with QIIME (UCLUST) or VSEARCH

csv file to graph
Graph CSV

Import csv file to graph

dada2 logo
NGMLST

NGMLST: Next Generation Multilocus Sequence Typing using DADA2

dada2 logo
DADA2

DADA2: Infer exact amplicon sequence variants (ASVs) from barcode sequences

structure data
Structure Files

Process data for structure tool

phyloseq
Phyloseq

Use phyloseq object to create graphs


Database search methods

taxonomy using UNITE ITS
BLAST Taxonomy

Select fungal taxonomy using UNITE or NCBI ITS database

query genbank
Query GenBank

Download FASTA and metadata for query of GenBank

Split combined ITS/LSU
ITSx

Split combined ITS/LSU into separate files with ITSx

query genbank for taxonomy
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


File manipulation and conversion

concat loci
Concatenate Loci

Concatenate several loci or generate single locus files

merge tables
Merge Vouchers

Merge two voucher tables into one

extend_sequence
Extend Sequence

Extend alignment with additional sequence

drap drop
Append Files

Append several text files into one file

venn diagram
Get Set Results

Get set results from lists in 2 files

newick to nexus
Nwk2nexus

Convert Phylogenetic tree from Newick to Nexus format

newick to nexus
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 test
Neutrality

Install locally and run neutrality test

mep archive
IMa3

Estimation of migration rates using Isolation-with-Migration (IMa3) models

structure plots
Structure

Show tree with structure plots

mep archive
IMgc

IMgc on CIPRES


Galaxy@NCSTATE

structure plots
Galaxy

Tools for population genetics and multi‑omics analysis


Utilities

pie chart
Piechart

Create pie charts

archive
Archive

Upload archive created by TBAS or DeCIFR utility

tree with collapse nodes
Collapse Tree

Collapse low support nodes on tree

telescope tree
Telescope Viewer

View telescope tree from MEP file

mep archive
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


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