Phylogenetic and network methods

patristic distance

Tree-Based Alignment Selector Toolkit

patristic distance

Create patristic distance rings with DendroPy.

MAFFT tool

Align sequence with MAFFT

denovo

Run de novo tree inference using RAxML.

tcs graph

Create graph with TCS.

trees 2 hypha tool

Show multiple node support values on tree using Mesquite Hypha.


Metabarcoding methods

meshclust

Create haplotype table with MeShClust.

cluster

Cluster sequences with QIIME (UCLUST) or VSEARCH.

csv file to graph

Import csv file to graph.

dada2 logo

NGMLST: Next Generation Multilocus Sequence Typing using DADA2

dada2 logo

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

structure data

Process data for structure tool.


Database search methods

taxonomy using UNITE ITS

Select fungal taxonomy using UNITE or NCBI ITS database.

query genbank

Download FASTA and metadata for query of GenBank.

Split combined ITS/LSU

Split combined ITS/LSU into separate files with ITSx

query genbank for taxonomy

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.


File manipulation and conversion

concat loci

Concatenate several loci or generate single locus files.

merge tables

Merge two voucher tables into one.

extend_sequence

Extend alignment with additional sequence

drap drop

Append several text files into one file.

venn diagram

Get set results from lists in 2 files.

newick to nexus

Convert Phylogenetic tree from Newick to Nexus format.

newick to nexus

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 locus files from annotations using phmmer and nhmmer output

Sort FASTA file by lengths


Population genetic methods

neutrality test

Install locally and run neutrality test.

mep archive

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

structure plots

Show tree with structure plots.


Galaxy@NCSTATE

structure plots

Tools for population genetics and multi‑omics analysis.


Utilities

pie chart

Create pie charts

archive

Upload archive created by TBAS or DeCIFR utility.

tree with collapse nodes

Collapse low support nodes on tree.

submit tree

Create files for T-BAS from MEP file.

server 2 server

Upload file directly from server to server

Big Tree Viewer.

telescope tree

View telescope tree from MEP file.

mep archive

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


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