Bioinformatics Tools

Useful Bioinformatics tools are open source and are easily available on net. Some of the commonly used tools ,links and their introduction is given below.
EMBOSS : This software is used for sequence alignment, protein structure prediction, motif finding, nucleotide sequence pattern analysis
Source: http://emboss.sourceforge.net
FASTA and SSEARCH : Fasta is used for the similarity search against protein database and SSEARCH is used a local alignment search tool and helpful to find best alignment score.
Source: http://www.ebi.ac.uk/Tools/sss/
BLAST : It is a basic local alignment search tool.
Source: http://www.ebi.ac.uk/Tools/sss/
GenePattern :It is a gene analysis platform that provides access to tools for gene expression and analysis. 
Source: http://www.broadinstitute.org/cancer/software/genepattern/
Biocarta : Brings the pathways and tools to observe how genes interact in dynamic graphical model.
Source: http://www.biocarta.com/
ClustalW2 : It is a multiple sequence alignment tool for DNA and protein sequences.It returns the best match scores by alignment of DNA sequences.
Source: http://www.ebi.ac.uk/Tools/msa/clustalw2/
Multiple Sequence Alignment tools: tools of MSA include MUSCLE, Clustal Omega, Kalign, MAFFT,T-Coffee,Mview. All of these alignment tools generally use two or more than two sequnces for the alignment to find out the best matches, evolutionary relationships amoung the sequences obtained from different organisms.
Source: http://www.ebi.ac.uk/Tools/msa/
MEME : It is a motif finding tool.This software tooks input in the form of DNA or protein sequence and give result in the form of possible motifs.
Source: http://meme.ebi.edu.au/meme/
ORF finder : This software tool is used to find the possible open reading frames of a given sequence.
Source: http://www.ncbi.nlm.nih.gov/projects/gorf/
LALIGN : Used for the local alignment of nucleotides and protein sequences.
Source: http://www.ebi.ac.uk/Tools/psa/lalign/