Changeset 8203 for branches/stable_5.0

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Timestamp:
10/11/11 10:01:42 (7 months ago)
Author:
westram
Message:
  • removed molphy (protml)
Location:
branches/stable_5.0
Files:
3 removed
7 modified

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Unmodified
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  • branches/stable_5.0/GDE/Makefile

    r7132 r8203  
    33        CLUSTAL/CLUSTAL.dummy  \ 
    44        SUPPORT/SUPPORT.dummy \ 
    5         MOLPHY/MOLPHY.dummy \ 
    65        AxML/AxML.dummy \ 
    76        RAxML/RAxML.dummy \ 

  • branches/stable_5.0/GDEHELP/ARB_GDEmenus.source

    r6069 r8203  
    5151menumeta:X 
    5252#include <fastdnaml.genmenu> 
    53 #include <molphy.genmenu> 
    5453 
    5554menu:Phylogeny max. Likelyhood 

  • branches/stable_5.0/GDEHELP/Makefile.helpfiles

    r5609 r8203  
    3636 
    3737$(GENHELPDEST)/dnaml.help: $(AXML_HELP) $(FASTDNAML_DOC) 
    38         ./genhelptree.sh $@ "$(subst .help,,$(notdir $@))" $(HEADER) $^ 
    39  
    40 PROTML=$(GDE)/MOLPHY/doc 
    41 PROTML_DOC_NAMES=protml protml_cli 
    42 PROTML_DOCS=$(addsuffix .doc,$(addprefix $(PROTML)/,$(PROTML_DOC_NAMES))) 
    43  
    44 $(GENHELPDEST)/protml.help: $(PROTML_DOCS) 
    4538        ./genhelptree.sh $@ "$(subst .help,,$(notdir $@))" $(HEADER) $^ 
    4639 

  • branches/stable_5.0/SH/README

    r7486 r8203  
    2929        arb_phyml                               wrapper for phyml 
    3030        arb_proml                               wrapper for proml 
    31         arb_protml                              wrapper for protml 
    3231        arb_protpars                            wrapper for protpars 
    3332        arb_raxml                               wrapper for raxml 

  • branches/stable_5.0/SOURCE_TOOLS/tabBrake.pl

    r5871 r8203  
    6666                                        'GDE/PHYML', 
    6767                                        'GDE/RAxML', 
    68                                         'GDE/MOLPHY', 
    6968                                        'GDE/SUPPORT', 
    7069                                        'GDE/PHYLIP', 

  • branches/stable_5.0/arb_LICENSE.txt

    r6142 r8203  
    236236        which is provided in 'lib/GPL.txt'. 
    237237 
    238     molphy 
    239  
    240         MOLPHY: A Computer Program Package for Molecular Phylogenetics 
    241          
    242         Readme 
    243                This is the MOLPHY (ProtML) distribution,  version 2.3. 
    244                 Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa. 
    245                                  All rights reserved. 
    246          
    247                 MOLPHY is a program package for MOLecular PHYlogenetics. 
    248          
    249         ProtML is a main program in MOLPHY for inferring evolutionary trees from 
    250         PROTein (amino acid) sequences by using the Maximum Likelihood method. 
    251          
    252         Programs (C language) 
    253           ProtML: Maximum Likelihood Inference of Protein Phylogeny 
    254           NucML:  Maximum Likelihood Inference of Nucleic Acid Phylogeny 
    255           ProtST: Basic Statistics of Protein Sequences 
    256           NucST:  Basic Statistics of Nucleic Acid Sequences 
    257           NJdist: Neighbor Joining Phylogeny from Distance Matrix 
    258         Utilities (Perl) 
    259           mollist:  get identifiers list        molrev:   reverse DNA sequences 
    260           molcat:   concatenate sequences       molcut:   get partial sequences 
    261           molmerge: merge sequences             nuc2ptn:  DNA -> Amino acid 
    262           rminsdel: remove INS/DEL sites        molcodon: get specified codon sites 
    263           molinfo:  get varied sites            mol2mol:  MOLPHY format beautifer 
    264           inl2mol:  Interleaved -> MOLPHY       mol2inl:  MOLPHY -> Interleaved 
    265           mol2phy:  MOLPHY -> Sequential        phy2mol:  Sequential -> MOLPHY 
    266           must2mol: MUST -> MOLPHY              etc. 
    267          
    268         MOLPHY is a free software, and you can use and redistribute it. 
    269         The programs are written in a standard subset of C with UNIX-like OS. 
    270         The utilities are written in the "Perl" (Ver.4.036) with UNIX-like OS. 
    271         MOLPHY has been tested on SUN4's (cc & gcc with SUN-OS 4.1.3) and 
    272         HP9000/700 (cc, c89 & gcc with HP-UX 9.05). 
    273         However, MOLPHY has NOT been tested on VAX, IBM-PC, and Macintosh. 
    274          
    275         NETWORK DISTRIBUTION ONLY: The latest version of MOLPHY is always available 
    276         by anonymous ftp in ftp.ism.ac.jp: /pub/ISMLIB/MOLPHY/. 
    277  
    278238    readseq 
    279239 

  • branches/stable_5.0/util/arb_srclst.pl

    r7023 r8203  
    157157 
    158158my @skipped_when_matchesFull = ( 
    159                                 qr/\/MOLPHY\/prot_tml\.h$/o, 
    160159                                qr/date\.xsl$/o, 
    161160                                qr/\/genhelp\/.*\.hlp$/o,