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protml_cli.doc

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This file has been automatically converted from the original documentation for easy use inside the ARB help system. Differences compared with the original documentation are unintentionally caused by the conversion process. In doubt please refer to the original documentation!

 

DOCUMENTATION

ProtML 2.3b3(July 1 1996) Maximum Likelihood Inference of Protein Phylogeny Copyright (C) 1992-1996 J. Adachi & M. Hasegawa. All rights reserved. Usage: protml [switches] sequence_file [topology_file] sequence_file = MOLPHY_format | Sequential(-S) | Interleaved(-I) topology_file = users_trees(-u) | constrained_tree(-e)

Model:

  •                               j  JTT (default)   -jf  JTT-F         Jones, Taylor & Thornton(1992)
                                
  •                               d  Dayhoff         -df  Dayhoff-F     Dayhoff et al.(1978)
                                
  •                               m  mtREV24         -mf  mtREV24-F     Adachi & Hasegawa(1995)
                                
  •                               p  Poisson         -pf  Proportional  (-f: with data Frequencies)
                                
  •                               r  users RSR       -rf  users RSR-F   (Relative Substitution Rate)
                                

Search strategy or Mode:

  •                               u  Users trees (need users_trees file)
                                
  •                               R  local Rearrangement search   -RX  LBP only
                                
  •                               e  Exhaustive search (with/without constrained_tree file)
                                
  •                               s  Star decomposition search (may not be the ML tree)
                                
  •                               q  Quick add OTUs search (may not be the ML tree)
                                
  •                               D  maximum likelihood Distance matrix --> NJDIST
                                

Others:

  •                               n num  retained top ranking trees (default -e:105,-q:50)
                                
  •                               P num  Per cent (default -e:30, if possible trees<=945 : 200)
                                
  •                               b  no RELL-BP          -M  Minimum evolution (with -e)
                                
  •                               S  Sequential format   -I  Interleaved format
                                
  •                               v  verbose to stderr   -i, -w  output some information