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Aligment
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Editing Alignments
GUIDANCE2
Weighting, filtering or masking unreliably aligned positions in sequence alignments before subsequent analysis
trimAl
Tool for automated alignment trimming
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Multiple Sequence Alignment
Clustal Omega
MSA program that uses seeded guide trees and HMM profile-profile techniques
EMBL-EBI
Multiple Sequence Alignment
MAFFT
Multiple alignment program for amino acid or nucleotide sequences
MultAlin
MSA from a group of related sequences using progressive pairwise alignments
PSSMSearch
Web application to discover novel protein motifs (SLiMs, mORFs, miniMotifs) and PTM sites
T-COFFEE
Align Protein, DNA and RNA sequences
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Structural Base Alignments
ESPRESSO
T-COFFEE is also able to combine sequence information with protein structural information
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Two Sequences Alignment
Dotlet JS
Comparing sequences by the diagonal plot method
LAST
LAST finds similar regions between sequences
LALIGN
Find multiple matching subsegments in two sequences
Pairwise Align DNA
Basic DNA pairwise alignment tool
Pairwise Align Protein
Basic protein pairwise alignment tool
Pairwise Alignment
Basic protein pairwise alignment tool
PRSS
Evaluates the significance of a protein sequence alignment