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fdnamlk.1e
Langue: en
Version: 08/04/2009 (ubuntu - 24/10/10)
Section: 1 (Commandes utilisateur)
Sommaire
NAME
fdnamlk - Estimates nucleotide phylogeny by maximum likelihoodSYNOPSIS
- 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.
COPYRIGHT
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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre