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What is sequence analysis?

Sequence analysis is a processes of analysing either DNA, RNA or protein sequences to understand its different features, structure and function. This process can involve sequence alignment and searching the sequence against known sequences in a database. As well as, profile comparison, sequence assemble and the gene or protein prediction. 

BLAST (basic local alignment search tool) is a pair-wise alignment tool for comparing primary biological sequences (nucleotide sequences/amino acid sequences) with a library or database of sequences. To enable the identification of database sequences that are similar to the query sequence above a certain threshold. 

MUSCLE (multiple sequence comparison by log-expectation) is a software for multiple sequence alignments of both protein and nucleotide sequences. 

 MAFFT (multiple alignment using fast Fourier transform) is a program to compare multiple sequence alignments of amino acid or nucleotide sequences.

CD-HIT is a program for clustering & comparing protein and nucleotide sequences.

Geneious Prime is a software which allows you to do sequence alignment, tree building, cloning and primer design. 

HMMER is a package for sequence analysis. It can be used to identify homologous protein or nucleotide sequences, and to for sequence alignments. It can detect homology by comparing a profile-HMM to either a single sequence or a database of sequences. 

Sequerome is a web-based sequence profiling tool. It allows for the integration of the results of a BLAST  report with external research tools and servers that undertake advanced sequence manipulations. It can work as a  front-end to BLAST queries and gives a simpler access to web-distributed resources for protein and nucleic acid analysis.

FASTA takes your nucleotide or amino acid sequence and searches a given sequence database by employing a local sequence alignment to find matches of similar databased sequences.