Align Multi-tool

Purpose: Simple manipulations of sequence alignments, including sorting, pruning, renaming, and slicing. See explanation.

	Sort		Prune		Rename		Slice & Concatenate

Input

Paste your alignment	>A1.AU.03.PS1044_Day0.DQ676872 ACCGAGCC-TGTAAACATTACTTGTATCAGACCTAACAACAATACAAGAA AAAGTGTACGT------ATAGGACCAGGACAAACATTCTATGCAACAGGT GAA------ATAATAGGGGATATTAGAAAAGCACATTGTGTGGTCAATAA AACAGAATGGAATAAAAATTTGAAAAAGGTAGTTGTACAATTAAGA---- --ACATACTTTAAG---AACAAAACAATAAGCTTTACTAACCAT---TCA GGAGGGGATCCAGAAGTTACAACACATAGTTTTAATTGTGGAGGAGAATT >A1.RW.92.92RW008.AB253421 GTCAAGCC-TGTGAAAATTAATTGTACCAGACCTAACAACAACACAAGAA CAAGTATACGT------ATAGGACCAGGACAATCATTCCATGCAACAGGT GAC------ATAATAGGGGATATCAGACAAGCACATTGCAATGTCAGTAG ATCAGAATGGAATGAAGCCTTACGACAGGTAGTTGAACAACTAAGA---- --GGACACTTTGGG---AACAAAACAATAATCTTTACTAACTCC---TCA GGAGGGGATATAGAAATCACAACACATAGTTTTAATTGTGGAGGAGAATT >A2.CD.97.97CDKTB48.AF286238 AATAAACC-TGTACCAATTAATTGTACCAGACCCAACAACAATACAAGAA AAAGTATACGC------TTTGGACCAGGACAGGCCTTCTATACAAATAAT AAC------ATAATAGGGGATATAAGACAAGCACATTGTAATATCAGCAT AACAGAATGGAATGCCACTCTAAAAAAGGTAGTTGAACAATTAAGA---- --GAACACTTCCCT---AATAAAACAATAATCTTTAATAGCTCC---TCA GGAGGGGACCTAGAAATTACAACACATAGTTTTAATTGTGGAGGAGAATT >A2.CY.94.94CY017_41.AF286237 ACTAAGCC-TGTACTAATTACTTGTATCAGACCCAACAACAATACAAGAA AAAGTATACGC------TTTGGACCAGGACAAGCCTTCTAT---ACAAAT GAA------ATAATAGGGGACATAAGACAAGCACATTGTAATATCAACAA AACATTATGGAATGACACTTTACAAAAGGTAGCTGAACAATTAAGA---- --GAGAAATTCCCT---AAGAAAACCATAATCTTTACTAACTCC---TCA GGAGGGGACCCAGAAATTACAACACTTAGTTTTAATTGTGCAGGAGAATT >B.FR.83.HXB2-LAI-IIIB-BRU.K03455 AACACATC-TGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAA AAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGA ---------AAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAG AGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGA---- --GAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCC---TCA GGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATT >B.NL.00.671_00T36.AY423387 AAGGAATC-TGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAA AAAGTATACAT------ATAGGACCAGGGAGAGCATTTTATGCAACAGGA GAA------ATAATAGGAGATATAAGACAAGCACATTGTAACCTTAGTAG AGCAAAATGGAATGACACTTTAAACCAGATAGTTGGAAAATTAAGA---- --GAATTATATAAG---AATAAAACAATAGTCTTTAATTCATCC---TCA GGAGGGGATCCAGAAATTGTAATGCACAGTTTTAATTGTAGAGGGGAATT >B.TH.90.BK132.AY173951 AAAGAACC-TGTAGAAATTAATTGTACAAGACCTAACAACTATACAAGGA AAAGAATAACT------ATGGGACCAGGGAGAGTATATTATACAACAGGA GAA------ATAATAGGAGATATAAGACGAGCACATTGTAACATTAGTAG CACAAAATGGAATAACACTTTAGGACAGATAGTTAAAAAATTAAAA---- --GAACAATTTAAC---AATAATACAATAGTCTTTAAGAAATCC---TCA GGAGGGGACCCAGAAATTGTAATGCACAGTTTTATTTGTGGAGGGGAATT >C.BR.92.BR025-d.U52953 AACGAATC-TGTAGAGATTAATTGTACGAGACCCAACAATAATACAAGAA AAAGTATAAGG------ATAGGACCAGGACAAGCATTCTATGCAACAGGA GAA------ATAATAGGAGATATAAGACAAGCACATTGTAACATTAGTAG AACAGCATGGAACAAAACTTTACAAGAGGTAGGTAAAAAATTAGCA---- --GAGCACTTCCCT---AATAAAGCAATAAAATTTGCAAAGCAC---TCA GGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTAGAGGAGAATT >C.ET.86.ETH2220.U46016 AATGAATC-TGTAGAAATTACTTGTACGAGACCCAGCAATAATACAAGAG AAAGTATAAGG------ATAGGACCAGGACAAACATTCTATGCAACAGGA GAC------ATAATAGGAGATATAAGACAAGCACATTGTAACATTAGTGA AGAAAAATGGAATAAAACTCTACAAAAGGTAAAGGAAAAATTACAA---- --AAGCACTTCCCT---AATAAAACAATAGAATTTAAGCCATCC---TCA GGAGGGGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATT >C.IN.95.95IN21068.AF067155 AATCAACC-TGTAGAAATTATGTGTACAAGACCCGACAATAATACAAGAA AAAGTATAAGG------ATAGGACCAGGACAAACATTCTATGCAACAGGA GAC------ATAATAGGAGACATAAGACAAGCACATTGTAACATTAGTGA AGATAAGTGGAATGAAACTTTACAAAATGTAAGTAAAAAGTTAGCA---- --GAACACTTCCCT---AATAAAACAATAATATTTAATTCATCA---TCA GGAGGGGACCTAGAAATTACAACACATAGCTTTAATTGTAGAGGAGAATT >D.CD.83.ELI.K03454 AATGAATC-TGTAAAAATTACCTGTGCAAGGCCCTATCAAAATACAAGAC AAAGAACACCT------ATAGGACTAGGGCAATCACTCTATACTACAAGA TCAAGATCAATAATAGGA---------CAAGCACATTGTAATATTAGTAG AGCACAATGGAGTAAAACTTTACAACAAGTAGCTAGAAAATTAGGA---- --ACCCTTCTTAAC---AAAACAATAATAAAGTTTAAACCATCC---TCA GGAGGGGACCCAGAAATTACAACACACAGTTTTAATTGTGGAGGGGAATT >D.TZ.01.A280.AY253311 AATGAGAC-TGTAAAAATTAATTGTACAAGGCCTAATAACAATACAAGAA AAGGTATACGT------ATAGGACCAGGGCAAACATTCTTTACAGCAGAG ---------GTAACAGGAGATATAAGAAAAGCATATTGTAACATTAGTGG AGCAGAATGGGATAAAACTTTACAACAAGTAGCTACAAAACTAGGA---- --GACCTTCTTAAC---AAGACAATAATAAATTTTAGTCCATCC---TCA GGAGGGGACCCAGAAATTACAACACATAGCTTTAATTGTGGAGGGGAATT >F1.BE.93.VI850.AF077336 AATGAATC-TGTACAGATTAATTGTACAAGACCCAACAACAATACAAGGA AAGGTATACAT------TTAGGACCAGGACAAACATTCTATGCAACAGGA GCA------ATAATAGGAGACATAAGAAAGGCACATTGTAACATTAGTGG AACACAATGGAATAACACTCTGGAGTATGTAAAGGCAGAATTAAAG---- --TCGCATTTCCCTAATAATACAGCAATAAAATTTAACCAATCC---TCA GGAGGGGACCTAGAAATTACAATGCATAGTTTTAATTGTAGAGGAGAATT >F1.BR.93.93BR020_1.AF005494 AATGAATC-TGTACAGATTAATTGTACAAGACCCAACAACAATACAAGAA AAAGAATATCT------TTAGGACCAGGACGAGTATTTTATACAACAGGA GAA------ATAATAGGAGACATCAGAAAGGCACATTGTAACGTTAGTGG AACACAATGGAGGAACACGTTAGCAAAGGTAAAGGCAAAGTTAGGG---- --TCTTATTTCCCT---AATGCAACAATAAAATTTAACTCATCC---TCA GGAGGGGACCTAGAAATTACAAGGCATAATTTTAATTGTATGGGAGAATT >F1.FI.93.FIN9363.AF075703 AATGAATC-TGTACAGATCAATTGTACAAGACCCAACAACAATACAAGAA AAAGTATACGT------ATAGGACCAGGACAATCATTTTATGCAACAGGA GAA------ATAATAGGAGACATAAGAAAGGCACATTGTAACATTAGTGG AGAACAATGGAATAAAACTTTAGACCGAGTAAAGGCAGAGTTAAAG---- --CTTCATTTT------AATAAAACAATACAATTTAACTCATCC---TCA GGAGGGGACCTAGAAATTACAATGCATAGTTTTAATTGTAGAGGAGAATT >F2.CM.02.02CM_0016BBY.AY371158 AATGAATC-AGTAAAAATTAACTGTACAAGACCCAACAACAATACAAGAA AAAGTATACGT------ATAGGACCAGGACAAGTATTTTATGCAACAGGT GAG------ATAATAGGAGACATAAGAAAGGCACATTGTACCATTAATGG AACACTGTGGAATGCAACTTTAAATAGGGTAGCTGCAGAGGTCAAA---- --AACCTCACT------AATATTACAATAAAATTTGAGCCATCA---TCA GGAGGGGACCTAGAAGTTACAACACATAGTTTTAGTTGTGGAGGAGAGTT >F2.CM.95.95CM-MP255.AJ249236 AATAGATC-TGTAATAATTGATTGTAGAAGACCCAACAACAATACAAGAA AAGGGATACGT------ATAGGACCAGGACAAACATTCTTTGCAACAGGT GAA------ATAATAGGGGATATAAGAAAGGCATATTGTAACATTAATAG AACACTGTGGAATGAAACTTTAAAAAATGTAAGTGGAGAGTTCAAA---- --AAACACTTC------AACTTCTCAGTAGCCTTTAATTCATCC---TCA GGAGGGGATGTAGAAATTACAACGCATAGTTTTAATTGTAGAGGAGAATT >F2.CM.95.95CM-MP257.AJ249237 AAAAATCC-TGTAAAAATTAATTGTACAAGACCCAACAACAATACAAGAA GAAGTATACAT------ATAGGACCAGGACGAGCATTCTATGCAACAGGT GAG------ATAATAGGAGATACAAGAAAGGCACATTGTAACATTAGTGA AAAACAGTGGTATGACACTTTAATAAAGATAGCTACAGAGTTCAAA---- --GACCAATAT------AATAAAACAGTAGGGTTTCAACCATCA---GCA GGAGGGGATCTAGAAATTACAACACATAGTTTTAATTGTAGAGGAGAATT >G.KE.93.HH8793_12_1.AF061641 AATGAAAC-TGTAGAAATTACGTGTGTCAGACCCAACAACAATACAAGAA AAAGTATACAC------CTCGGGCCAGGACAAGCGCTCTATGCAACAGGG GAC------ATAATAGGAAATATAAGACAGGCACATTGTGATGTTAGTGG AAGAAATTGGAGTAACATGATAGAGAAGGTAAAAGCACAACTAAGA---- --AAAATCTTT------AACAAGACCATAACCTTTGACTCATCT---GCA GGAGGGGACCTAGAAATTACAACACATAGTTTTAATTGTAGGGGAGAATT >G.NG.92.92NG083_JV10832.U88826 AATAATAG-TATAGAAATTAATTGTATCAGACCCAATAACAATACAAGAA AAAGTATACCA------ATCGGACCAGGACAAGCGTTCTATGCAACAGGT GAT------ATAATAGGAGACATAAGACAAGCACATTGTAATGTTAGTAG AATAAAATGGAGGGAGATGTTAAAGAATGTCACAGCACAGCTAAGG---- --AAAATCTATAAT---AATAAGAACATAACCTTTAACTCATCT---GCA GGAGGGGACCTAGAAATTACAACACATAGTTTCAATTGTAGAGGAGAGTT >H.BE.93.VI991.AF190127 AATGAACC-TGTACAAATTAACTGTACCAGAACAGGCAATAATACGAGAA AAAGTATACGT------ATAGGGCCAGGACAAGCATTCTATGCAACAGGT GAC------ATCATAGGAGATATAAGACGAGCATATTGTAATATTAGTGG AAAACAATGGAATGAGACCTTACACAAGGTAATCACCAAATTAGGA---- --AGCTACTTTGAC---AATAAAACAATAATTTTACAACCACCC---GCA GGAGGGGATATAGAGATTATAACACATAGTTTTAATTGTGGAGGAGAGTT >H.BE.93.VI997.AF190128 GATAGTCC-TATAGAAATTACCTGTACCAGACCTAACAATAATACAAGAA AAGGTATACAT------TTCGGGCCAGGGCAAGCATTCTATGCAACAGGT GAT------ATCATAGGAAACATAAGACAAGCACATTGTAATGTTAGTGA AGAGAAATGGAATAAGACTTTACAACAGATAGCTACACAATTAAGT---- --AAATACTTTGTC---AATAGAACATTAATTTTTAAACCACAC---TCA GGAGGGGACCTGGAAGTTACAACACATAGTTTTAACTGTAGAGGAGAATT >H.CF.90.056.AF005496 AAGACACC-AGTAAACATTACATGTACCAGGCCTAACAATAATACGAGAA CAAGTATACAT------TTAGGGCCAGGACGAGCATTCTATGCAACAGGT GAC------ATCATAGGAGATATAAGACAAGCACATTGTAATATTAGTAG AACAGACTGGAATAAGACTTTACACCAGGTAGTTACACAATTAGGA---- --ATACACTTGAAC---AATAGAACAATAAGCTTTAAGCCAAAC---TCA GGAGGGGACATGGAAGTTAGAACACATAGTTTTAATTGTAGAGGAGAATT >J.CD.97.J_97DC_KTB147.EF614151 AACCAAAC-TGTAGAAATCAATTGTACCAGACCCGCCAACAATACAAGAA AGGGTATACCC------ATAGGACCAGGGCAAGTGCTATATGCAACAGGT GCA------GTAATAGGAAACATAAGACAAGCACATTGTAACATTAGTGG AGTAAAATGGAATAATACTTTACATAAAGTAGCTGAAGAATTAAGAGAAC AAGAACACTTTAAG---AATAAAACAATAGTCTTTGCACCAGCAAATTCA GGAGGGGACATAGAAATTATGATGCATACTTTTAATTGTGGAGGAGAGTT >J.SE.93.SE9280_7887.AF082394 AATAAAAC-TGTAGAAATTGTGTGTTACAGACCTAATAACAATACAAGGA AAGGTATACAC------ATGGGACCAGGACAAGTGCTCTACGCAACAGGA GAA------ATAATAGGAAATATAAGAGAAACACATTGTAACATTAGTGA AAGAGATTGGAGTAACACTTTACGTAGAGTAGCTACAAAACTAAGA---- --GAACACTTT------AATAAAACAATAAACTTTACATCACCC---TCA GGAGGGGATATAGAAATTGTGACACATAGTTTTAATTGTGGAGGAGAATT >K.CD.97.97ZR-EQTB11.AJ249235 AATGAAGC-TGTAGAAATTAATTGTACAAGGCCAAGCAACAATACAAGAA AAAGTATACAT------ATAGGACCAGGAAGAGCATTCTATGCAACAGGT GAC------ATAATAGGAGATATAAGGCAGGCGCATTGTAACATTAGCGG AGGACAGTGGAATAAAACTGTAAACCAAGTAAAGAAAGAATTAGGA---- --AAACACTTT------AACAAAACAATAATATTTCAACCATCC---TCA GGAGGGGACCCACAAGTCACAAGGCACATTTTTAACTGTAGAGGAGAATT >K.CM.96.96CM-MP535.AJ249239 AATGAAAC-TGTACAAATTAATTGTACAAGGCCAAACAACAATACAAGAA AAAGTATACAT------ATGGGACCAGGAAAAGCATTCTATACAACAGGT GAT------ATAATAGGAGATATAAGACAGGCACATTGCAACATTAGTGG AGAAAAATGGAACATGACTTTAAGCAGAGTAAAGGAAAAGCTAAAA---- --GAACATTTTAAG---AATGGAACAATAACATTTAAACCACCAAACCCA GGAGGAGACCCAGAAATTCTAACGCACATGTTTAATTGTGCAGGAGAATT >50_A1D.GB.10.12792.JN417240 -GCCAGCCCTGTGAACATTAGTTGTGTTAGACCTAACAACAATACAAGGA AAAGTGTACGT------ATAGGGCCAGGACAAACATTCTATGCAAATAAT GAC------ATAATAGGGAATATAAGACAAGCACACTGTAATGTCAGTGG ATCAAAATGGAATAAAACTTTACAACAGGTAGCT-AGGAAATTAGGGAAC -----CTTCTTAAC---CAGACAACAATAATTTTTAAACCATCC---TCA GGAGGGGATCCAGAAATCACAATGCATAGTTTTAATTGTGGAGGAGAATT >A1U.NG.10.10NG040248.KX389608 -AATAAGGCTGTAGAAATTAATTGTATCAGGCCTAACAACAATACAAGAA AAAGCATACAT------ATAGGACCAGGACAAGCATTCTATGCAACAGGT GAA------ATAATAGGGGATATAAGACAAGCACAGTGTGAGGTCAATAA AACTAAATGGGATAACATGTTACAACGGGTAGCT-GCACAATTAGGAGAA -----CTCCTTAAC---AAAACAGAAATAAACTTTAATCAATCC---GCA GGAGGAGATATAGAAATTACAACACATAGTTTTAATTGTGGGGGAGAATT
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Sort by
Sequence name		HIV/SIV subtype (works when part of names contains subtype)      Subtype is in field of names delimited by      (See explanation for ordering and naming conventions.) Full name in ascending descending Part of name. Delimit names with    sort by field of names in ascending descending [add more levels to sort]
Newick tree		Create tree (works only for a small set of sequences) Tree tool PAUP*         (NJ) Model  Total: number of pairwise character differences  Mean: mean number of pairwise character differences  Abs: absolute distances  P: P-distance  JC: Jukes and Cantor (1969)  F81: Felsenstein (1981)  TajNei: Tajima and Nei (1984)  K2P: Kimura (1980)  F84: Felsenstein (1984)  HKY85: Hasegawa, Kishino, and Yano (1985)  K3P: Kimura (1981)  TamNei: Tamura and Nei (1993)  GTR: general time-reversible  LogDet: log-determinant (Steel, 1994; Lockhart et al., 1994) or paralinear (Lake, 1994)  Upholt: restriction-site distance of Upholt (1977)  NeiLi: restriction-site distance of Nei and Li (1979)  Mean: mean number of pairwise character differences Site rates Equal Gamma Shape FastTree   Model  JC: Jukes-Cantor (default)  GTR: General-time-reversible  Jones-Taylor-Thorton 1992 (default)  Whelan-And-Goldman 2001 # of categories     Use gamma for final tree Join option    NJ   BioNJ Outgroup Use my tree
Similarity		Hamming distance from the top sequence in ascending descending order Gaps    Count    Discount
Sequence		5' starting point    3' starting point    Length (without gaps) Alignment column at     1st sequence residue at          Ascending      Descending
Custom list
Pick top sequence		HIV reference sequences. Accessions (K03455 or M33262) are included in seq name Current 1st sequence Name None

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Export names
Export		Save sequence names to text file
Check uniqueness
Check		Find duplicate names
Replace names with
HIV database field values		Accession must be in input seq name to search database Seq name is accession Accession is in field of names delimited by Numbering fields composing a new name Subtype Country Year Name Accession Patient code SE ID Patient ID Field separator . _ - Missing character for unavailable values - X x (empty) NA
Sequential numbers		Starting number     Prefix     Suffix
Custom lookup table

Options

Prune sequnces by
Name match		(for pattern, simple regex allowed) Match type Exact word Pattern   case insensitive Match against full name field of names delimited by
Custom list
Invert		Remove other than the above specified sequences
Squeeze gaps		Delete columns that are entirely gaps Preserve codons (delete gaps in triplets)

Upload alignment file(s)	sample_input1.fasta      sample_input2.fasta