This is the command fdnamle that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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