fpromlke - Online in the Cloud

PROGRAM:

NAME

fpromlk - Protein phylogeny by maximum likelihood

SYNOPSIS

fpromlk -sequence seqsetall -intreefile tree [-ncategories integer] -rate array
-categories properties [-weights properties] -lengths boolean [-model list]
[-gamma list] -gammacoefficient float -ngammacat integer -invarcoefficient float
-ninvarcat integer -invarfrac float -nhmmcategories integer -hmmrates array
-hmmprobabilities array -adjsite boolean -lambda float -njumble integer
-seed integer -global boolean [-outgrno integer] -outfile outfile [-trout toggle]
-outtreefile outfile [-printdata boolean] [-progress boolean] [-treeprint boolean]
[-hypstate boolean]

fpromlk -help

DESCRIPTION

fpromlk is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Phylogeny:Molecular sequence" command group(s).

OPTIONS

Input section
-sequence seqsetall
File containing one or more sequence alignments

-intreefile tree

-ncategories integer
Default value: 1

-rate array

-categories properties

-weights properties

Additional section
-lengths boolean
Default value: N

-model list
Default value: Jones-Taylor-Thornton

-gamma list
Default value: n

-gammacoefficient float
Default value: 1

-ngammacat integer
Default value: 1

-invarcoefficient float
Default value: 1

-ninvarcat integer
Default value: 1

-invarfrac float
Default value: 0.0

-nhmmcategories integer
Default value: 1

-hmmrates array
Default value: 1.0

-hmmprobabilities array
Default value: 1.0

-adjsite boolean
Default value: N

-lambda float
Default value: 1.0

-njumble integer

-seed integer
Default value: 1

-global boolean
Default value: N

-outgrno integer

Output section
-outfile outfile

-trout toggle
Default value: Y

-outtreefile outfile

-printdata boolean
Default value: N

-progress boolean
Default value: Y

-treeprint boolean
Default value: Y

-hypstate boolean
Default value: N

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