Alignment Software

 

Sequence alignments are either local or global. Local alignments find the best matching segments between two sequences and form the basis of the database search programs. Global alignments find the best match over the total length of both sequences. Alignments may be performed on a pairwise basis, across multiple sequences or they can involve the alignment of a sequence to a previously aligned set of sequences (sometimes called a profile).
Local GlobalMultiple
Profile Editing & PresentingRelated


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Local Alignments
Program nameSourceDescription
BestFit GCG Smith-Waterman local alignments
FrameAlign GCG Local (or Global) alignment of a protein sequence to all frames of a nucleic acid sequence.
lalign FastA Local sequence alignment program that displays the N-best local alignments.
matcher EMBOSS Local alignment of two sequences
sip4 Staden Compares pairs of sequences. It includes dot plots, finding matching words, global and local optimal alignments and statistical evaluation of matches.
supermatcher EMBOSS Finds a match of one sequence against one or more sequences(for Large Sequences)
water EMBOSS Smith-Waterman local alignment.
Global Alignments
Program nameSourceDescription
align FastA Optimal global alignment of two sequences
align0 FastA As align, but does not penalize for end-gaps.
Gap GCG Needleman-Wunsch global alignment
needle EMBOSS Needleman-Wunsch global alignment.
sip4 Staden Compares pairs of sequences. It includes dot plots, finding matching words, global and local optimal alignments and statistical evaluation of matches.
stretcher EMBOSS Global alignment of two sequences.
Multiple Alignments
Program nameSourceDescription
clustalw igmbc-fr Multiple alignment program (command line based).
clustalx igmbc-fr Multiple alignment program (X-windows based).
emma EMBOSS Multiple alignment program
PileUp GCG Multiple sequence alignment from progressive (tree based), pairwise alignments
Profile Alignments
Program nameSourceDescription
ProfileGap GCG Makes an optimal alignment between a profile and one or more sequences.
ProfileMake GCG Creates a position-specific scoring table or profile.
ProfileSegments GCG Makes optimal alignments from similar segments found by ProfileSearch.
prophecy EMBOSS Creates matrices/profiles from multiple alignments
prophet EMBOSS Gapped alignment for profiles
Editing and Presenting Alignments
Program nameSourceDescription
flalign FastA Plots lalign local alignments to a GCG Figure file.
Gapshow GCG Graphical representation of an alignment.
LineUp GCG Editor for multiple alignments.
plalign FastA Plots lalign local alignments to a postscript file.
Pretty GCG Displays multiple sequence alignments and calculates a consensus sequence.
PrettyBox GCG Displays multiple sequence alignments in PostScript format, using shading.
prettyplot EMBOSS Displays aligned sequences, with colouring and boxing.
Alignment Related Programs
Program nameSourceDescription
CompTable GCG Create a (simplified) scoring matrix.
Consensus GCG Generates a consensus sequence for short nucleotide sequences.
est2genome EMBOSS Align EST and genomic DNA sequences
FitConsensus GCG Finds matches to a consensus sequence matrix.
Plotsimilarity GCG Plots a running average of similarity among sequences in a multiple alignment.
seqmatchall EMBOSS All against all word based sequence comparison


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