Input Sequences DNA or Protein sequences in Fasta, GenBank, EMBL, Swiss-Prot, or Clustalw format. Upload local file or Enter text or Load example —— DNA Examples —— antibody-4x1864 antibody-2x1439 —— AA Examples —— asparaginase-7x360 glutaminase-26x315 insulin-8x110 protease-7x305
Alignment Methods clustal select options msa select options muscle select options probcons select options dialign select options poa select options tcoffee select options
clustal select options msa select options muscle select options probcons select options dialign select options poa select options tcoffee select options
clustal Options Pairwise Alignment Slow Accurate Gap opening penalty [0-100]: -pwgapopen Gap Extension Penalty [0-100]: -pwgapext DNA weight matrix: -pwdnamatrix IUB CLUSTALW(1.6) Protein comparison matrix: -pwmatrix Blosum 30 PAM 350 Gonnet 250 Identity (-quicktree) Fast Approximate Gap Penalty [0-500]: -pairgap Number of top diagonals (1 to 4000): -topdiags Window size (1 to 50): -window K-tuple: -ktuple 1 2 3 4 Multiple Alignment Gap opening penalty [0-100]: -gapopen Delay divergent sequences: -maxdiv % DNA weight matrix: -dnamatrix IUB CLUSTALW(1.6) Protein comparison matrix: -matrix Blosum series PAM series Gonnet series Identity matrix Gap Extension Penalty [0-100]: -gapext Negative matrix: -negative off Transition weight (DNA)(0-1): -transweight Protein Gap Residue-specific penalties: -nogap on Hydrophilic residues: -hgapresidues Gap separation distance[0-100]: -gapdist Hydrophilic penalties: -nohgap on End gap separation penalty: -endgaps off dialign Options Diagonal threshhold: -thr Iterative scoring: -it off Overlap weights: -ow (always) (#seq<35) -iw (never) Clustering method: -max_link -min_link UPGMA Asterisk mask: -mask off Maximum fragment length: -lmax Minimum similarity value: -smin msa Options Terminal gap charge: -g (same as internal gaps) no charge Alignment cost: -b (unweighted sum) weights by rationale-2 Maximal score: -d muscle Options Maximum iteration: -maxiters Diagonal optimization: -diags off poa Options Aggressive fusion: -fuseall off Heavy bundling: -hb off -hbmin % Alignment: -do_global off -do_progressive off probcons Options Consistency: -c [0-5] Iterative refinement: -ir off Pre-training: -pre off Viterbi coding: -viterbi off tcoffee Options Gap penalties: -gapopen -gapext -cosmetic_penalty Terminal gaps: -tgmode gapopen and gapext gapopen only no penalty Dynamic programming: -dp_mode gotoh_pair_wise myers_miller_pair_wise fasta_pair_wise cfasta_pair_wise Normalize scoring: -do_normalise -ndiag -diag_mode complete diag best segment Output Formats (shading details) Output shading: Consensus shaded by identity by similarity show conserved reverse Protein colored Output order: as input as aligned
Pairwise Alignment Slow Accurate Gap opening penalty [0-100]: -pwgapopen Gap Extension Penalty [0-100]: -pwgapext DNA weight matrix: -pwdnamatrix IUB CLUSTALW(1.6) Protein comparison matrix: -pwmatrix Blosum 30 PAM 350 Gonnet 250 Identity (-quicktree) Fast Approximate Gap Penalty [0-500]: -pairgap Number of top diagonals (1 to 4000): -topdiags Window size (1 to 50): -window K-tuple: -ktuple 1 2 3 4 Multiple Alignment Gap opening penalty [0-100]: -gapopen Delay divergent sequences: -maxdiv % DNA weight matrix: -dnamatrix IUB CLUSTALW(1.6) Protein comparison matrix: -matrix Blosum series PAM series Gonnet series Identity matrix Gap Extension Penalty [0-100]: -gapext Negative matrix: -negative off Transition weight (DNA)(0-1): -transweight Protein Gap Residue-specific penalties: -nogap on Hydrophilic residues: -hgapresidues Gap separation distance[0-100]: -gapdist Hydrophilic penalties: -nohgap on End gap separation penalty: -endgaps off
Diagonal threshhold: -thr Iterative scoring: -it off Overlap weights: -ow (always) (#seq<35) -iw (never) Clustering method: -max_link -min_link UPGMA Asterisk mask: -mask off Maximum fragment length: -lmax Minimum similarity value: -smin
Terminal gap charge: -g (same as internal gaps) no charge Alignment cost: -b (unweighted sum) weights by rationale-2 Maximal score: -d
Maximum iteration: -maxiters Diagonal optimization: -diags off
Aggressive fusion: -fuseall off Heavy bundling: -hb off -hbmin % Alignment: -do_global off -do_progressive off
Consistency: -c [0-5] Iterative refinement: -ir off Pre-training: -pre off Viterbi coding: -viterbi off
Gap penalties: -gapopen -gapext -cosmetic_penalty Terminal gaps: -tgmode gapopen and gapext gapopen only no penalty Dynamic programming: -dp_mode gotoh_pair_wise myers_miller_pair_wise fasta_pair_wise cfasta_pair_wise Normalize scoring: -do_normalise -ndiag -diag_mode complete diag best segment