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HIV sequence database



Align Multi-tool

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

  Sort   Prune   Rename  
Input
Paste your alignment

[Sample Input]
Or upload sequence file
Options
Sort by  
HIV/SIV subtype
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  Subtype is in field of names delimited by
(See explanation for ordering and naming conventions.)
Newick tree
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  Create tree (works only for a small set of sequences)
Tree tool PAUP* Model
Site rates Equal Gamma Shape
FastTree   Model
# of categories     Use gamma for final tree
Join option    NJ   BioNJ
Outgroup
Use my tree
      
      
Similarity
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  Hamming distance from the top sequence in ascending desending order
Gaps    Count    Discount
Sequence
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5' starting point    3' starting point    Length (without gaps)
Alignment column at     1st sequence residue at    
     Ascending
     Descending
Sequence name
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  Full name in ascending descending
Part of name. Delimit names with   
sort by field of names in ascending descending [add more levels to sort]
Custom list
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Pick top sequence
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  HIV reference sequences. Accessions (K03455 or M33262) are included in seq name
Current 1st sequence
Name
None
Options
Export names  
Export Save sequence names to text file
Check uniqueness  
Check Find duplicate names
Replace names with  
HIV database
field values
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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
Sequential numbers
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  Starting number     Prefix     Suffix
 
Custom lookup table
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Options
Prune sequnces by  
Name match
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  (for pattern, simple regex allowed)
Match type Exact word
Pattern   case insensitive
Match against full name
field of names delimited by
Custom list
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Invert
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  Remove other than the above specified sequences
 
Squeeze gaps
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  Delete columns that are entirely gaps
Preserve codons (delete gaps in triplets)

last modified: Thu Feb 15 12:32 2018


Questions or comments? Contact us at seq-info@lanl.gov.

 
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