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Welcome to TrEase 2.0

( Inferring phylogenetic trees with ease... )

By default, this pipeline searches reference sequences using BLAST for user-provided fasta sequences from the local NR database downloaded from NCBI, and retrieves the sequence data of the three top hits. The unique sequences from the BLAST top hits, along with the input sequences are oriented according to the first sequence of the user provided dataset, then are aligned using MAFFT and the MSA is trimmed from both ends according to the first sequence. Further a phylogenetic tree is construction using RAxML-NG software.
Please Note: Each module, i.e. homologous sequence search, sequence alignment and phylogeny building, of the pipeline can be used independently.

Upload sequences for generating Phylogenetic tree

Input Sequence Data in FASTA format

Advanced Options (optional)

Look for reference sequences using Blast Yes No

Exclude environmental samples: Select reference from:

Select Algorithm: E-value:
Number of reference for each sequence:

(The NT database was updated on 27th May, 2025.)

Build Multiple Sequence Alignment Yes No

Orient all sequences according to the first sequence Yes No

Mafft Select Model:

Muscle Maximum number of iterations:

Prank Select alignment type: ?

Trim ends of MSA according to the first sequence Yes No

Alignment refinement using Gblock Yes No

Maximum Number Of Contiguous Nonconserved Positions
Minimum Length Of A Block
Allowed Gap Positions

Construct Phylogenetic tree Yes No

RAxML-NG

Select algorithm: ? Select bootstrap value:

FastME

Select algorithm: Select bootstrap value:

MrBayes

Select model: Number of generations: Percentage of Trees to discard:

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