Man pages sections > man1 > fdnaml

fdnaml - Estimates nucleotide phylogeny by maximum likelihood

FDNAML(1e) EMBOSS Manual for Debian FDNAML(1e)

NAME

fdnaml - Estimates nucleotide phylogeny by maximum likelihood

SYNOPSIS

fdnaml -sequence seqsetall -intreefile  tree [-ncategories  integer] -rate  array -categories properties [ -weights properties] -lengths  boolean [-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 [ -outgrno integer] [-rough boolean] -outfile outfile [ -trout toggle] -outtreefile outfile [-printdata  boolean] [-progress  boolean] [-treeprint  boolean] [-hypstate  boolean]
fdnaml -help

DESCRIPTION

fdnaml 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
Weights file

Additional section

-lengths boolean
Default value: N
-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
-outgrno integer
-rough boolean
Default value: Y

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

fdnaml 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.
 
08/11/2010 PHYLIPNEW 3.69+20100721