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// test for "no tree" below has to match ../../TEMPLATES/arb_global_defs.h@NO_TREE_SELECTED
#define PHYML_CALL(seqtype) \
( GOTO_LOCAL_DIR;GEN_PHYLIP(infile) && \
RUN_IN_WINDOW(if [ "$TREE" != "tree_?????" -a ! -z "$TREE" ]; then arb_export_tree $TREE > input_tree.in; INPUT_TREE_PARAM=-uinput_tree.in; fi; \
(phyml \
--input=infile \
--datatype=seqtype \
--model=$MODEL \
-f$BASEFREQEST \
--bootstrap=$BOOTSTRAP \
--search=$SEARCH \
-o$PARAM_OPTIMIZATION \
--r_seed=$RAND_SEED \
--pinv=$PROPINVAR \
--alpha=$ALPHA \
$INPUT_TREE_PARAM \
$CUSTOM_PARAMS || STOP_ON_FAILURE(phyml_20130708)) && \
mv infile_phyml_tree.txt outtree && \
$DISPLAY_FUNC))&
#ifdef PHYML_DNA
item: PHYML-20130708 (DNA)
seqtype: N
itemmethod:PHYML_CALL(nt)
itemmeta: P
#else
item: PHYML-20130708 (Amino acids)
seqtype: A
itemmethod:PHYML_CALL(aa)
itemmeta: Y
#endif
itemhelp:phyml-20130708.help
// $INPUT_TREE_PARAM is either empty or contains -uinput_tree.in depending on the selection of the starting tree
arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
#ifdef PHYML_DNA
argchoice:ARB ('tree_phyml_'):arb_read_tree tree_phyml_$$ outtree "PRG=phyml-20130708 FILTER=$FILTER STYPE=DNA"
#else
argchoice:ARB ('tree_phyml_'):arb_read_tree tree_phyml_$$ outtree "PRG=phyml-20130708 FILTER=$FILTER STYPE=AA"
#endif
argchoice:TextEdit:arb_textedit outfile &
argchoice:Treetool:treetool outtree
arg:MODEL
argtype:choice_menu
arglabel:Nuc. substitution model
#ifdef PHYML_DNA
argchoice:GTR:GTR
argchoice:HKY85 (default):HKY85
argchoice:JC69:JC69
argchoice:K80:K80
argchoice:F81:F81
argchoice:F84:F84
argchoice:TN93:TN93
#else
argchoice:LG (default):LG
argchoice:WAG:WAG
argchoice:JTT:JTT
argchoice:MtREV:MtREV
argchoice:Dayhoff:Dayhoff
argchoice:DCMut:DCMut
argchoice:RtREV:RtREV
argchoice:CpREV:CpREV
argchoice:VT:VT
argchoice:Blosum62:Blosum62
argchoice:MtMam:MtMam
argchoice:MtArt:MtArt
argchoice:HIVw:HIVw
argchoice:HIVb:HIVb
#endif
arg:PARAM_OPTIMIZATION
argtype:choice_menu
arglabel:Specific parameter optimization
argchoice:Optimize tree topology, branch len, rate params:tlr
argchoice:Optimize tree topology and branch length:tl
argchoice:Optimize branch length and rate parameters:lr
argchoice:Optimize branch length:l
argchoice:Optimize rate parameters:r
argchoice:Do not optimize any parameters:n
arg:PROPINVAR
argtype:text
arglabel:Proportion of invariable sites\n(Range [0..1] or e to get the maximum likelihood estimate)
argtext:e
arg:ALPHA
argtype:text
arglabel:Distribution of the gamma distribution shape parameter\n(Positive value or e to get the maximum likelihood estimate)
argtext:e
arg:RAND_SEED
argtype:text
arglabel:Pseudo random number generator seed
argtext:424242
arg:BASEFREQEST
argtype:choice_menu
arglabel:Base frequency estimates
argchoice:Empirical:e
#ifdef PHYML_DNA
argchoice:ML:m
#else
argchoice:Model:m
#endif
arg:BOOTSTRAP
arglabel:Bootstrap
argtype:choice_menu
argchoice:(default) approximate Bayes branch supports:-5
argchoice:neither approximate likelihood ratio test nor bootstrap values are computed:0
argchoice:approximate likelihood ratio test returning aLRT statistics:-1
argchoice:approximate likelihood ratio test returning Chi2-based parametric branch supports:-2
argchoice:SH-like branch supports alone:-4
argchoice:20 boostrap replicates:20
argchoice:50 boostrap replicates:50
argchoice:100 boostrap replicates:100
argchoice:200 boostrap replicates:200
argchoice:500 boostrap replicates:500
argchoice:1000 boostrap replicates:1000
argchoice:10000 boostrap replicates:10000
arg:SEARCH
argtype:choice_menu
arglabel:Tree topology search operation option
argchoice:NNI (default, fast):NNI
argchoice:SPR (a bit slower than NNI):SPR
argchoice:BEST (best of NNI and SPR search):BEST
arg:TREE
argtype:tree
arglabel:Starting tree
argchoice:?????
arg:CUSTOM_PARAMS
argtype:text
arglabel: Custom parameters
argtext:
in:TmpInputFile
informat:genbank
insave:
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