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clustal-omega-wrapper

A simple node module that wraps the functionalities of Clustal Omega multiple sequence alignment program

Visit official Clustal Omega web site to learn more about it. http://www.clustal.org/omega/

Install

You can install clustal-omega-wrapper by running,

npm install clustal-omega-wrapper

You can download Clustal Omega executable by running,

node util/downloader.js

It will download the Clustal Omega executable to util/bin folder

Usage

Align an unaligned sequence file

• .alignSeqFile (inputFile, outputFormat, callback)
  callback passed (err, stdOut, stdErr)

  var clustalOmega = require('clustalo-wrapper');
  var inputFile = 'samples/example.fasta';
  var outputType = 'fasta';
   
  clustalOmega.alignSeqFile(inputFile, outputType, function(err,stdout,stdErr){
      if(err){
          console.log(stdErr);
      }else{
          console.log(stdout);
      }
  });
      

Align an unaligned input string of sequences of FASTA format

• .alignSeqString (input, outputFormat, callback)
  callback passed (err, output)

    var clustalOmega = require('clustalo-wrapper');
    var outputType = 'fasta';
    var input = '>test1\n' +
              'ACDEFGHIKLMNPQRSTVWY\n' +
              '>test2\n' +
              'XXXXACDEFGHIMNXXXPQR\n' +
              '>test3\n' +
              'ACDEFGHILMNXXXXXPQRS\n' +
              '>test4\n' +
              'XXXACDEFGHIKLMNPQRST';
    clustalOmega.alignSeqString(input,outputType,function(err,data){
        if(err){
            console.log(err);
        }else{
            console.log(data);
        }
    });
   
   

Align an unaligned seq file and an HMM

• .alignSeqWithHmm (inputFile, inputHmmFile, outputFormat, callback)
  callback passed (err, output)

Align an unaligned seq file and a profile

• .alignSeqWithProfile (inputFile, inputProfile, outputFormat, callback)
  callback passed (err, output)

Align two profiles

• .alignTwoProfiles (profile1, profile2, outputFormat, callback)
  callback passed (err, output)

The output can be in any of the following formats (set 'outputFormat' to one of the following)

  *  fasta
  *  clustal
  *  msf
  *  phylip
  *  selex
  *  stockholm
  *  vienna

You can specify a custom execution path where the clustal omega executable is placed

var clustalOmega = require('clustalo-wrapper');
var customExecPath = 'Downloads/bin';
var outputType = 'fasta';
 
clustalOmega.setCustomLocation('../../Downloads');