Sequence Analysis

A collection of articles explaining operations of biological sequences for sequence analysis.

Homology search against a local dataset using NCBI-BLAST+ command-line tool


NCBI-BLAST+ [1] command-line tool offers multiple functions to be performed on a large dataset of sequences. Previously, we have shown how to blast against a local dataset of sequences. This article will explain the search of homologous sequences for a query sequence against a local database of sequences and how to obtain the top 100 hits out of the searched results. Keep Reading

How to use Clustal Omega and MUSCLE command-line tools for multiple sequence alignment?


Clustal Omega [1,2] and MUSCLE are bioinformatics tools that are used for multiple sequence alignment (MSA). In one of our previous articles, we explained the usage of the ClustalW2 command-line tool for MSA and phylogenetic tree construction. In this article, we will use Clustal Omega and MUSCLE for MSA exploring other arguments that facilitate different output formats. Keep Reading

Multiple Sequence Alignment and Phylogenetic Tree construction using ClustalW2 command-line tool

ClustalW2 is a bioinformatics tool for multiple sequence alignment of DNA or protein sequences. It can easily align sequences and generate a phylogenetic tree online ( However, in some cases, we need to perform these operations on a large number of FASTA sequences using the command-line tool of ClustalW2 [1]. Keep Reading

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