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fdnaml
Estimates nucleotide phylogeny by maximum likelihood

Standard (Mandatory) qualifiers:
[-sequence] seqsetall File containing one or more sequence
alignments
[-intreefile] tree Phylip tree file (optional)
[-outfile] outfile [*.fdnaml] Phylip dnaml program output file

Additional (Optional) qualifiers (* if not always prompted):
-ncategories integer [1] Number of substitution rate categories
(Integer from 1 to 9)
* -rate array Rate for each category
* -categories properties File of substitution rate categories
-weights properties Weights file
* -lengths boolean [N] Use branch lengths from user trees
-ttratio float [2.0] Transition/transversion ratio (Number
0.001 or more)
-[no]freqsfrom toggle [Y] Use empirical base frequencies from
seqeunce input
* -basefreq array [0.25 0.25 0.25 0.25] Base frequencies for A
C G T/U (use blanks to separate)
-gamma menu [Constant rate] Rate variation among sites
(Values: g (Gamma distributed rates); i
(Gamma+invariant sites); h (User defined HMM
of rates); n (Constant rate))
* -gammacoefficient float [1] Coefficient of variation of substitution
rate among sites (Number 0.001 or more)
* -ngammacat integer [1] Number of categories (1-9) (Integer from
1 to 9)
* -invarcoefficient float [1] Coefficient of variation of substitution
rate among sites (Number 0.001 or more)
* -ninvarcat integer [1] Number of categories (1-9) including one
for invariant sites (Integer from 1 to 9)
* -invarfrac float [0.0] Fraction of invariant sites (Number
from 0.000 to 1.000)
* -nhmmcategories integer [1] Number of HMM rate categories (Integer
from 1 to 9)
* -hmmrates array [1.0] HMM category rates
* -hmmprobabilities array [1.0] Probability for each HMM category
* -adjsite boolean [N] Rates at adjacent sites correlated
* -lambda float [1.0] Mean block length of sites having the
same rate (Number 1.000 or more)
* -njumble integer [0] Number of times to randomise (Integer 0
or more)
* -seed integer [1] Random number seed between 1 and 32767
(must be odd) (Integer from 1 to 32767)
* -global boolean [N] Global rearrangements
-outgrno integer [0] Species number to use as outgroup
(Integer 0 or more)
-[no]rough boolean [Y] Speedier but rougher analysis
-[no]trout toggle [Y] Write out trees to tree file
* -outtreefile outfile [*.fdnaml] Phylip tree output file
(optional)
-printdata boolean [N] Print data at start of run
-[no]progress boolean [Y] Print indications of progress of run
-[no]treeprint boolean [Y] Print out tree
-hypstate boolean [N] Reconstruct hypothetical sequence

Advanced (Unprompted) qualifiers: (none)
General qualifiers:
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose