MSA
2.1
multiple sequence alignment
S. F. Altschul
msa
msa
perl
"msa"
0
seqs
Sequences File
perl
" $value"
2
8
control
Control parameters
optimal
Turns off the optimal multiple alignment
perl
($value)? " -m":""
0
1
forcedres
forced aligned residues file (see the documentation)
perl
($value)? " -f $value" : ""
1
Cost
Cost parameters
endgap
charges terminal gaps the same as internal gaps
perl
($value)? " -g":""
0
1
unweight
cost = unweighted sum
perl
($value)? " -b":""
0
1
maxscore
maximum score of an optimal multiple alignment
perl
(defined $value)? " -d$value" : ""
1
epsilons
Epsilons file (see the documentation)
perl
($value)? " -e $value" : ""
1
costs
Costs file (see the documentation)
perl
($value)? " -c $value" : ""
1
output
Output parameters
quiet
suppress verbose output
perl
($value)? " -o":""
1