Changeset 8205 for trunk

Timestamp:

10/11/11 10:30:51 (7 months ago)

Author:

westram

Message:

merge from stable_5.0 [8203]

• removed molphy (protml)

Location:

trunk

Files:

• GDE/MOLPHY (deleted)
• GDE/Makefile (modified) (2 diffs)
• GDEHELP/ARB_GDEmenus.source (modified) (1 diff)
• GDEHELP/MENUS/molphy.menu (deleted)
• GDEHELP/Makefile.helpfiles (modified) (1 diff)
• Makefile (modified) (1 diff)
• SH/README (modified) (1 diff)
• SH/arb_protml (deleted)
• SOURCE_TOOLS/tabBrake.pl (modified) (1 diff)
• arb_LICENSE.txt (modified) (1 diff)

trunk/GDE/Makefile

@@ -3 +3 @@
         CLUSTAL/CLUSTAL.dummy  \
         SUPPORT/SUPPORT.dummy \
-        MOLPHY/MOLPHY.dummy \
         AxML/AxML.dummy \
         RAxML/RAxML.dummy \
@@ -54 +53 @@
 endif
 
-proto: MOLPHY/MOLPHY.proto
-
 depends: $(ARCHS:.dummy=.depend)
 

trunk/GDEHELP/ARB_GDEmenus.source

@@ -51 +51 @@
 menumeta:X
 #include <fastdnaml.genmenu>
-#include <molphy.genmenu>
 
 menu:Phylogeny max. Likelyhood

trunk/GDEHELP/Makefile.helpfiles

@@ -36 +36 @@
 
 $(GENHELPDEST)/dnaml.help: $(AXML_HELP) $(FASTDNAML_DOC)
-        ./genhelptree.sh $@ "$(subst .help,,$(notdir $@))" $(HEADER) $^
-
-PROTML=$(GDE)/MOLPHY/doc
-PROTML_DOC_NAMES=protml protml_cli
-PROTML_DOCS=$(addsuffix .doc,$(addprefix $(PROTML)/,$(PROTML_DOC_NAMES)))
-
-$(GENHELPDEST)/protml.help: $(PROTML_DOCS)
         ./genhelptree.sh $@ "$(subst .help,,$(notdir $@))" $(HEADER) $^
 

trunk/Makefile

@@ -1446 +1446 @@
                 $(ARCHS_PT_SERVER:.a=.proto) \
                 SERVERCNTRL/SERVERCNTRL.proto \
-                GDE/GDE.proto \
                 SL/SL.proto \
 

trunk/SH/README

@@ -29 +29 @@
         arb_phyml                               wrapper for phyml
         arb_proml                               wrapper for proml
-        arb_protml                              wrapper for protml
         arb_protpars                            wrapper for protpars
         arb_raxml                               wrapper for raxml

trunk/SOURCE_TOOLS/tabBrake.pl

@@ -67 +67 @@
                                         'GDE/PHYML',
                                         'GDE/RAxML',
-                                        'GDE/MOLPHY',
                                         'GDE/SUPPORT',
                                         'GDE/PHYLIP',

trunk/arb_LICENSE.txt

@@ -236 +236 @@
         which is provided in 'lib/GPL.txt'.
 
-    molphy
-
-        MOLPHY: A Computer Program Package for Molecular Phylogenetics
-        
-        Readme
-               This is the MOLPHY (ProtML) distribution,  version 2.3.
-                Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa.
-                                 All rights reserved.
-        
-                MOLPHY is a program package for MOLecular PHYlogenetics.
-        
-        ProtML is a main program in MOLPHY for inferring evolutionary trees from
-        PROTein (amino acid) sequences by using the Maximum Likelihood method.
-        
-        Programs (C language)
-          ProtML: Maximum Likelihood Inference of Protein Phylogeny
-          NucML:  Maximum Likelihood Inference of Nucleic Acid Phylogeny
-          ProtST: Basic Statistics of Protein Sequences
-          NucST:  Basic Statistics of Nucleic Acid Sequences
-          NJdist: Neighbor Joining Phylogeny from Distance Matrix
-        Utilities (Perl)
-          mollist:  get identifiers list        molrev:   reverse DNA sequences
-          molcat:   concatenate sequences       molcut:   get partial sequences
-          molmerge: merge sequences             nuc2ptn:  DNA -> Amino acid
-          rminsdel: remove INS/DEL sites        molcodon: get specified codon sites
-          molinfo:  get varied sites            mol2mol:  MOLPHY format beautifer
-          inl2mol:  Interleaved -> MOLPHY       mol2inl:  MOLPHY -> Interleaved
-          mol2phy:  MOLPHY -> Sequential        phy2mol:  Sequential -> MOLPHY
-          must2mol: MUST -> MOLPHY              etc.
-        
-        MOLPHY is a free software, and you can use and redistribute it.
-        The programs are written in a standard subset of C with UNIX-like OS.
-        The utilities are written in the "Perl" (Ver.4.036) with UNIX-like OS.
-        MOLPHY has been tested on SUN4's (cc & gcc with SUN-OS 4.1.3) and
-        HP9000/700 (cc, c89 & gcc with HP-UX 9.05).
-        However, MOLPHY has NOT been tested on VAX, IBM-PC, and Macintosh.
-        
-        NETWORK DISTRIBUTION ONLY: The latest version of MOLPHY is always available
-        by anonymous ftp in ftp.ism.ac.jp: /pub/ISMLIB/MOLPHY/.
-
     readseq