Compute Multiple Sequence Alignments — multi

This function takes a FASTA file containing DNA or amino acid sequences that shall be aligned and computes a multiple alignment using a defined multiple alignment tool.

Usage

multi_aln(
  file,
  tool,
  get_aln = FALSE,
  path = NULL,
  multi_aln_name = NULL,
  params = NULL,
  quiet = FALSE,
  clean_folders = FALSE
)

Arguments

file: a character string specifying the path to the file storing the sequences in FASTA format.
tool: a character string specifying the program that should be used: "clustalw", "t_coffee", "muscle", "clustalo", and "mafft".
get_aln: a logical value indicating whether the produced alignment should be returned.
path: a character string specifying the path to the multiple alignment program (in case you don't use the default path).
multi_aln_name: a character string specifying the name of the stored alignment file. Default is multi_aln_name = NULL denoting a default name: 'toolname.aln' .
params: a character string listing the input paramters that shall be passed to corresponding alignment tool specified in the tool argument. Default is NULL, implicating that a set of default parameters is used when running the correponding tool, e.g. clustalw. Example: params = "-PWMATRIX=BLOSUM -TYPE=PROTEIN" for tool = "clustalw.
quiet: a logical value specifying whether the output of the corresponding multiple alignment tool shall be printed out to the console. Default is quiet = FALSE.
clean_folders: a boolean value spefiying whether all internall folders storing the output of used programs shall be removed. Default is clean_folders = FALSE.

Value

In case the argument get_aln is set TRUE, an object of class alignment of the seqinr package is returned.

Details

This function provides an interface between R and common multiple alignment programs such as "clustalw", "t_coffee", "muscle", "clustalo", and "mafft".

CLUSTALW :

Different operating systems perform different execution calls to the clustalw program:
- MacOS: 'clustalw2'
- Linux: 'clustalw'
- Windows: 'clustalw2.exe'
In case you use the default path to the clustalw program, depending on your operating system, the following calls to clustalw should work properly on your system:
- MacOS: system("clustalw2 -help")
- Linux: system("clustalw -help")
- Windows: system("clustalw2.exe -help")
In case these procedures don't work properly, please use the path argument to specify the 'clustalw' execution path on your system:
- MacOS: system("path/to/clustalw/clustalw2 -help")
- Linux: system("path/to/clustalw/clustalw -help")
- Windows: system("path/to/clustalw/clustalw2.exe -help")
T_COFFEE :

In case you use the default path to the t_coffee program, the following calls to clustalw should work properly on your system:

system("t_coffee -version")

In case this procedures doesn't work properly, please use the path argument to specify the 't_coffee' execution path on your system:

system("path/to/t_coffee/t_coffee -version")
MUSCLE :

In case you use the default path to the muscle program, the following calls to muscle should work properly on your system:

system("muscle -help")

In case this procedures doesn't work properly, please use the path argument to specify the 'muscle' execution path on your system:

system("path/to/muscle/muscle -help")
CLUSTALO :

In case you use the default path to the clustalo program, the following calls to clustalo should work properly on your system:

system("clustalo --help")

In case this procedures doesn't work properly, please use the path argument to specify the 'clustalo' execution path on your system:

system("path/to/clustalo/clustalo --help")
MAFFT :

In case you use the default path to the mafft program, the following calls to mafft should work properly on your system:

system("mafft -help")

In case this procedures doesn't work properly, please use the path argument to specify the 'mafft' execution path on your system:

system("path/to/mafft/mafft -help")

Note

Note that when using the clustalw.params, ... parameters, make sure the corresponding alignment tool returns a file in clustal format *.aln. This is only important when get_aln = TRUE.

References

CLUSTALW:

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.

https://www.clustal.org/clustal2/

https://www.ebi.ac.uk/jdispatcher/
T_COFFEE

T-Coffee: A novel method for multiple sequence alignments. Notredame, Higgins, Heringa, JMB, 302(205-217). 2000.

https://tcoffee.readthedocs.io/en/latest/

https://tcoffee.readthedocs.io/en/latest/tcoffee_technical_documentation.html
MUSCLE:

Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797.

Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, (5) 113.

https://www.drive5.com/muscle/

https://www.drive5.com/muscle/manual/
CLUSTALO:

Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soeding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75

https://www.ebi.ac.uk/jdispatcher/msa/clustalo/

https://www.genome.jp/tools-bin/clustalw
MAFFT :

Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780) MAFFT multiple sequence alignment software version 7: improvements in performance and usability.

https://mafft.cbrc.jp/alignment/software/

https://mafft.cbrc.jp/alignment/software/manual/manual.html

https://mafft.cbrc.jp/alignment/software/tips0.html

Author

Hajk-Georg Drost and Sarah Scharfenberg

Examples

if (FALSE) { # \dontrun{

# CLUSTALW Example:

# in case the default execution path of clustalw runs properly on your system
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "clustalw", 
          get_aln = TRUE)

# in case the default execution path of clustalw is not set within the default path
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'), 
          tool    = "clustalw", 
          get_aln = TRUE, 
          path    = "path/to/clustalw/")

# running clustalw using additional parameters
# details: system("clustalw2 -help")
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "clustalw", 
          get_aln = TRUE, 
          params  = "-PWMATRIX=BLOSUM -TYPE=PROTEIN")
          
          
# T_COFFEE Example:

# in case the default execution path of t_coffee runs properly on your system
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "t_coffee", 
          get_aln = TRUE)

# in case the default execution path of t_coffee is not set within the default path
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "t_coffee", 
          get_aln = TRUE, 
          path    = "path/to/t_coffee/")

# running t_coffee using additional parameters
# details: https://tcoffee.readthedocs.io/en/latest/tcoffee_technical_documentation.html
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "t_coffee", 
          get_aln = TRUE,
          params  = "-mode expresso")
          


# MUSCLE Example:  

# in case the default execution path of muscle runs properly on your system
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "muscle", 
          get_aln = TRUE)

# in case the default execution path of muscle is not set within the default path
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "muscle", 
          get_aln = TRUE, 
          path    = "path/to/muscle/")

# running muscle using additional parameters
# details: https://www.drive5.com/muscle/manual/
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "muscle", 
          get_aln = TRUE,
          params  = "-diags -clwstrict") 
          

# CLUSTALO Example:  

# in case the default execution path of clustalo runs properly on your system
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "clustalo", 
          get_aln = TRUE)

# in case the default execution path of clustalo is not set within the default path
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "clustalo", 
          get_aln = TRUE, 
          path    = "path/to/clustalo/")

# running clustalo using additional parameters
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "clustalo", 
          get_aln = TRUE,
          params  = "--outfmt clu")         
          
          
                                            
# MAFFT Example:  

# in case the default execution path of mafft runs properly on your system
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "mafft", 
          get_aln = TRUE)

# in case the default execution path of mafft is not set within the default path
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "mafft", 
          get_aln = TRUE, 
          path    = "path/to/mafft/")

# running mafft using additional parameters
# details: https://mafft.cbrc.jp/alignment/software/manual/manual.html
multi_aln(file    = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
          tool    = "mafft", 
          get_aln = TRUE,
          params  = "--maxiterate 1 --clustalout")         
          
                                                                                  
} # }