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fdnamlk.1e

Langue: en

Version: 08/04/2009 (ubuntu - 24/10/10)

Section: 1 (Commandes utilisateur)

NAME

fdnamlk - Estimates nucleotide phylogeny by maximum likelihood

SYNOPSIS

fdnamlk -sequence seqsetall -intreefile tree [-ncategories integer] -rate array -categories properties [-weights properties] [-ttratio float] [-freqsfrom toggle] -basefreq array [-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 -lengths boolean -outfile outfile [-trout toggle] -outtreefile outfile [-printdata boolean] [-progress boolean] [-treeprint boolean] [-hypstate boolean]
fdnamlk -help

DESCRIPTION

fdnamlk

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

-ttratio float

Default value: 2.0

-freqsfrom toggle

Default value: Y

-basefreq array

Default value: 0.25 0.25 0.25 0.25

-gamma list

Default value: Constant rate

-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

-lengths boolean

Default value: N

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

BUGS

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

fdnamlk is fully documented via the tfm(1) system.

AUTHOR

Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

Wrote the script used to autogenerate this manual page.

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.

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