Welcome to TrEase.

( Inferring phylogenetic trees with ease... )

By default, this pipeline searches reference sequences (using BLAST software) for user provided fasta sequences from the local NR database (downloaded from NCBI), and retrives the sequence data of the three top hits. The unique sequences from the blast top hits, along with the input sequences are subjected to multiple sequence alignment using mafft and further phylogenetic tree constructed (using RAxML software) and all the result files are provided to be downloaded.
Please Note: Each part of the pipeline can be used independently.

Upload sequences for generating Phylogenetic tree

Copy and Paste your sequences below in FASTA format
Or upload the fasta text file from your computer.

Advanced Options (optional)

Look for reference sequences using Blast (e-value: 10e-30)

Select Algorithm
Number of reference for each sequence Exclude unidentified & uncultured species
select reference from top hits select reference from different individual species
(The NT database was updated on 28th June, 2024.)

Build Multiple Sequence Alignment

Mafft  Select model
muscle  Maximum number of iterations
prank  Select alignment type ?

Alignment refinement

Do you want to select conserved blocks of MSA using gblock?

Construct Phylogenetic tree

RAxML
 Select algorithm  ?
 Select Bootstrap value
FastTree
 Select algorithm

MrBayes
 Select model
 No. of generations  Percentage of tree to discard

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