|
Local Alignments |
| Program name | Source | Description |
|---|
| 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 name | Source | Description |
|---|
| 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 name | Source | Description |
|---|
| 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 name | Source | Description |
|---|
| 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 name | Source | Description |
|---|
| 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 name | Source | Description |
|---|
| 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 |
