EMBOSS explorer

fdnaml

Estimates nucleotide phylogeny by maximum likelihood (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section

Select an input sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
Select an input file::
Number of substitution rate categories
Rate for each category
File of substitution rate categories:
Weights file:
Additional section
Use branch lengths from user trees?
Transition/transversion ratio
Use empirical base frequencies from seqeunce input?
Base frequencies for A C G T/U (use blanks to separate)
Rate variation among sites
Coefficient of variation of substitution rate among sites
Number of categories (1-9)
Coefficient of variation of substitution rate among sites
Number of categories (1-9) including one for invariant sites
Fraction of invariant sites
Number of HMM rate categories
HMM category rates
Probability for each HMM category
Rates at adjacent sites correlated?
Mean block length of sites having the same rate
Number of times to randomise
Random number seed between 1 and 32767 (must be odd)
Global rearrangements?
Species number to use as outgroup
Speedier but rougher analysis?
Output section
Write out trees to tree file?
Print data at start of run?
Print indications of progress of run?
Print out tree?
Reconstruct hypothetical sequence?
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.