BLOSUM62: BLOSUM62 matrix
In LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Description Usage Format Source Examples

A substitution matrix used for sequence alignment of proteins. In LowMACA, it is used to calculate the trident conservation score.

1	data("BLOSUM62")

A squared numeric matrix with aminoacids as rownames and colnames

BLOSUM62 from NCBI

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#Load BLOSUM62 and show its structure
data(BLOSUM62)
str(BLOSUM62)

Checking if clustalo is in the PATH...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base).
BEGIN failed--compilation aborted.
Warning messages:
1: In .ClustalChecks(ClustalCommand = "clustalo") :
  Clustal Omega is not in the PATH:
You can either change clustalo command using lmParams function or use the web service. See ?setup
2: In system(paste(perl, "-MXML::Simple -e 1"), intern = TRUE) :
  running command '/usr/bin/perl -MXML::Simple -e 1' had status 2
3: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
  XML::Simple module for perl is not installed. 
            If you don't want to install a local clustal omega and use the web service, XML::Simple is required

 int [1:25, 1:25] 4 -1 -2 -2 0 -1 -1 0 -2 -1 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:25] "A" "R" "N" "D" ...
  ..$ : chr [1:25] "A" "R" "N" "D" ...