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.

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.

PHYLIPNEW 3.69+20100721                            08/11/2010                                         FDNAML(1e)