MultipleAlignment 프로그램.

 * http://www.ebi.ac.uk/clustalw/ (웹서비스)
 * http://bimas.dcrt.nih.gov/clustalw/clustalw.html (관련 페이퍼)

관련정보
 * Program server in [[KRIBB]] : http://plant.pdrc.re.kr/gene/align/clustalW.html 
 * OperatingSystem별 다운로드 : ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/
 * BioPython에서 사용하기 : [BioPythonTutorial/CookBook/Alignment] 

== Standalone manual ==

=== Sequence Input From Disc ===

모든 입력서열은 하나의 파일내에 존재해야한다. 다음의 7가지 서열포맷을 자동인식한다.
 * NBRF-[[PIR]]
 * [[EMBL]]-SwissProt
 * FastaFormat (Pearson)
 * Clustal (*.aln)
 * [[GCG]]-MSF (Pileup)
 * [[GCG]]9-RSF
 * GDE flat file

=== Multiple Alignments ===

입력서열에 대해 MultipleAlignment를 실행한다. 세부메뉴가 있다.
 1. Do complete multiple alignment now (Slow/Accurate)
 1. Produce guide tree file only
 1. Do alignment using old guide tree file
 1. Toogle Slow/Fast pairwise alignments = SLOW
 1. PairwiseAlignment parameters
  * Slow/Accurate alignments
   1. Gap open penalty : 10.00
   1. Gap extension penalty : 0.10
   1. Protein weight matrix : Gonnet series
   1. DNA weight matrix : IUB
  * Fast/Approximate alignments
   1. Gap penalty : 3
   1. K-tuple (word) size : 1
   1. No. of top diagonals : 5
   1. Window size : 5
  * Toggle Slow/Fast pairwise alignments = SLOW
 1. MultipleAlignment parameters
  1. Gap open penalty : 10.00
  1. Gap extension penalty : 0.20
  1. Delay divergent sequences : 30%
  1. DNA transitions weight : 0.50
  1. Protein weight matrix : Gonnet series
  1. DNA weight matrix : IUB
  1. Use negative matrix : OFF
  1. Protein Gap Parameters
   1. Toggle Residue-specific penalties : ON
   1. Toggle Hydrophilic penalties : ON
   1. Hydrophilic residues : GPSNDZEKR
   1. Gap separation distance : 4
   1. Toggle end gap separation : OFF
 1. Reset gaps before alignment? = OFF
 1. Toggle screen display = ON
 1. Output format options
  1. Toggle FastaFormat output = OFF
  1. Toggle Clustal format output = ON
  1. Toogle GCG/MSF format output = OFF
  1. Toogle PHYLIP format output = OFF
  1. Toogle NEXUS format output = OFF
  1. Toogle GDE format output = OFF
  1. Toogle GDE output case = LOWSE
  1. Toogle ClustalW sequence numbers = OFF
  1. Toogle output order = ALIGNED 
  1. Toogle parameter output = OFF
  1. Toogle sequence range numbers = OFF

=== Profile / Structure Alignments ===

[Profile]/Structure alignment를 수행한다. 세부메뉴는
 1. Input 1st. profile
 1. Input 2nd. profile/sequences
 1. Align 2nd. profile to 1st. profile
 1. Align sequences to 1st. profile (Slow/Accurate)
 1. Toggle Slow/Fast pairwise alignments = SLOW
 1. Pairwise alignment parameters
 1. Multiple alignment parameters
 1. Secondary structure options
  1. Use profile 1 secondary structure / penalty mask = YES
  1. Use profile 2 secondary structure / penalty mask = YES
  1. Output in alignment = secondary structure
  1. Helix gap penalty : 4
  1. Strand gap penalty : 4
  1. Loop gap penalty : 1
  1. Secondary structure terminal penalty : 2
  1. Helix terminal positions within : 3   outside : 0
  1. Strand terminal positions within : 1   outside : 1

=== Phylogenetic trees ===

PhylogeneticTree를 생성한다. 세부메뉴로
 1. Input an alignment
 1. Exclude positions with gaps? = OFF
 1. Correct for multiple substitutions? = OFF
 1. Draw tree now
 1. Bootstrap tree
 1. Output format options
  1. Toggle Clustal format tree output = OFF
  1. Toogle [[PHYLIP]] format tree output = ON
  1. Toggle [[PHYLIP]] distance matrix output = OFF
  1. Toggle Nexus format tree output = OFF
  1. Toogle [[PHYLIP]] boostrap positions = BRANCH LABELS / NODE LEBELS

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CategoryProgramBio