Phylogenomic Tools

A collection of tools for comparative phylogenomics analyses, phylodiversity estimates, visualization tools of underlying genomic structure and phylogenomic conflict, and pre-processing of sequence data for phylogenetic analyses.

tcs graph

Create graph with TCS.

patristic distance

Create patristic distance rings with DendroPy.

structure plots

Show tree with structure plots.

taxonomy using UNITE ITS

Select fungal taxonomy using UNITE ITS database.

pie chart

Create pie charts

Split combined ITS/LSU

Split combined ITS/LSU into separate files with ITSx

concat loci

Concatenate several loci.

merge tables

Merge two voucher tables into one.

archive

Upload archive created by TBAS or DeCIFR utility.

drap drop

Concatenate several text files into one file.

venn diagram

Get set results from lists in 2 files.

dada2 logo

DADA2: Infer amplicon sequence variants (ASVs) across samples

dada2 logo

NGMLST: Next Generation Multilocus Sequence Typing using DADA2

tree with collapse nodes

Collapse low support nodes on tree.

csv file to graph

Import csv file to graph.

meshclust

Create haplotype table with MeShClust.

cluster

Cluster sequences with QIIME (UCLUST) or VSEARCH.

denovo

Run de novo tree inference using RAxML.

newick to nexus

Convert Phylogenetic tree from Newick to Nexus format.

structure data

Process data for structure tool.

submit tree

Create files for T-BAS from MEP file.

MAFFT tool

Align sequence with MAFFT

server 2 server

Upload file directly from server to server

trees 2 hypha tool

Upload multiple trees to create input file for Mesquite Hypha.

MEP file

View and download data from MEP file.

telescope tree

View telescope tree from MEP file.

neutrality test

Install locally and run neutrality test.

query genbank

Download FASTA and metadata for query of GenBank.

mep archive

Retrieve MEP files from archive by run id

mep archive

ima3