DeCIFR

Tree-Based Alignment Selector Toolkit

Create patristic distance rings with DendroPy.

Align sequence with MAFFT

Run de novo tree inference using RAxML.

Create graph with TCS.

Show multiple node support values on tree using Mesquite Hypha.

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.

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.

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 locus files from annotations using phmmer and nhmmer output

Install locally and run neutrality test.

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

Show tree with structure plots.

Tools for population genetics and multi‑omics analysis.

Create pie charts

Upload archive created by TBAS or DeCIFR utility.

Collapse low support nodes on tree.

Create files for T-BAS from MEP file.

Upload file directly from server to server

Big Tree Viewer.

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

Run treepic on files from genetree output