Sequences alignments and comparisons

• Sequences consensus and Sequences comparaison
• Pairwise comparisons
• Multiple alignments
• Alignments of structures
• Alignments display
• HMM (Hidden Markov Models)

• Sequences consensus and Sequences comparaison

EMBOSS
• merger: Merge two overlapping sequences.
• megamerger: Merge two large overlapping nucleic acid sequences.
• cons: Creates a consensus from multiple alignments.
• diffseq: Find differences (SNPs) between nearly identical sequences.

• Pairwise comparisons

BL2SEQ

• bl2seq: aligning two sequences with the NCBI-Blast2 algorithm.




WISE

• wise: Comparison of a protein and a DNA sequence (genomic or cDNA).




COMBAT

• combat: COMBined AlignmenT: Comparison of coding DNA.




EMBOSS

• needle: Needleman-Wunsch global alignment.
• stretcher: Finds the best global alignment between two sequence.
• water: Smith-Waterman local alignment.
• matcher: Finds the best local alignments between two sequences.
• supermatcher: Finds a match of a large sequence against one or more sequences.
• seqmatchall: All-against-all comparison of a set of sequences
• wordmatch: Finds all exact matches of a given size between 2 DNA sequences.
• wordfinder: Match large sequences against one or more other sequence s
• prettyplot: Replacement for EGCG's prettyplot. Also to provide text output from sequence alignments.
• polydot: Multiple sequence rapid dotplot. A replacement for EGCG's polydot.
• dotmatcher: Creates a dot plot of two sequences.
• dottup: Displays a wordmatch dotplot of two sequences.
• dotpath: Displays a non-overlapping wordmatch dotplot of two sequences.
• est2genome: Align EST and genomic DNA sequences.

• Multiple alignments

MUSCLE

• muscle: Multiple alignment software for protein and nucleotide sequences.




CLUSTALW

• clustalw-multialign: Do full multiple alignment.
• clustalw-profile: Merge two alignments by profile alignment.
• clustalw-sequence: Sequentially add profile sequences to profile alignment.




DCA

• dca: Divide-And-Conquer multiple sequence alignment.




PIMA

• pima: Pattern-Induced Multi-sequence Alignment.




DIALIGN

• dialign: DNA and protein sequences comparison and multiple alignment.




TREEALIGN

• treealign: A Unified Approach to Alignments and Phylogenies.




COMALIGN

• comalign: Multiple nucleic sequences alignment.




EMBOSS

• edialign: Local multiple alignment of sequences
• plotcon: Plots the quality of conservation of a multiple sequence alignment.
• tranalign: Align nucleic coding regions given the aligned proteins.

• Alignments of structures

COSA

• cosa: Clustal Ouput Structural Analysis.

• Alignments display

BOXSHADE

• boxshade: Multiple alignment viewer.




MVIEW

• mview: Multiple alignment viewer.




EMBOSS

• extractalign: Extract regions from a sequence alignment
• infoalign: Information on a multiple sequence alignment
• prettyplot: Multiple alignment viewer.
• showalign: Multiple alignment viewer.




VIENNARNA

• rnaalifold: Calculate secondary structures for a set of aligned RNAs

• HMM (Hidden Markov Models)

HMMER

• hmmalign: Align sequences whith a profile HMM.
• hmmbuild: Builds a HMM from a multiple sequence alignment
• hmmcalibrate: Takes an HMM and empirically determines parameters that are used to make searches more sensitive, by calculating more accurate expectation value scores (E-values).
• hmmconvert: Convert a model into different formats.
• hmmemit: Emit sequences probabilistically from a profile HMM