item:FastTree2 (nucleotide)
itemmeta:F
seqtype:N
itemmethod:(GOTO_LOCAL_DIR; \
            arb_sed 's/#/>/' <TmpInputFile | \
            arb_sed 's/%/>/' | \
            arb_sed 's/"/>/'| \
            arb_sed 's/@/>/' | \
            arb_sed '/^[^>]/ y/./-/' > fasttree_in; \
            RUN_IN_WINDOW(( ($ARBHOME/bin/FastTree $FAST $MLMODEL -nt fasttree_in > fasttree_out || STOP_ON_FAILURE(FastTree)) && \
                           $DISPLAY_FUNC));)&


arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:Load into ARB ('tree_fasttree_//'):$ARBHOME/bin/arb_read_tree tree_fasttree_$$ fasttree_out "PRG=FastTree$FAST FILTER=$FILTER MODEL=!$MLMODEL"
argchoice:Treetool:treetool fasttree_out


arg:FAST
argtype:choice_menu
arglabel:speed up the neighbor joining phase\n(recommended for >50,000 sequences)
argchoice:No:
argchoice:Yes:-fastest

arg:MLMODEL
argtype:choice_menu
arglabel:ML Model
argchoice:Jukes-Cantor:
argchoice:GTR:-gtr


in:TmpInputFile
informat:flat
insave:

//----------------------

#define PREPARE_MRBAYES_INFILE(INFILE) \
        ( \
                arb_sed -i '/LABELPOS/d' INFILE     `#MrBayes does not understand the LABELPOS command, therefore it is removed.` && \
                arb_sed -i '/EQUATE/d' INFILE       `#MrBayes does not support EQUATE macros, remove them.` && \
                arb_sed -i '/OPTIONS/,/;/d' INFILE  `#MrBayes does not support the OPTIONS block, remove it. (delete everything between OPTIONS and ';')` \
        )

#define NEXUS2NEWICK(FROM,APPENDTO) ($ARBHOME/bin/arb_nexus2newick.awk FROM >> APPENDTO || STOP_ON_FAILURE(arb_nexus2newick))

item:MrBayes
itemmeta:B
seqtype:*
itemmethod:(GOTO_LOCAL_DIR; \
            GEN_NEXUS(mrbayes_in) && \
            PREPARE_MRBAYES_INFILE(mrbayes_in) && \
            ( \
                `# append the mrbayes command block to the nexus file`; \
                COMMAND="begin mrbayes; \
                         set autoclose=yes nowarn=yes; \
                         lset nst=$NST rates=$RATES ngammacat=$NGAMMACAT; \
                         mcmc ngen=$NGEN nchains=$NCHAINS temp=$TEMP samplefreq=$SAMPLEFREQ burninfrac=$BURNINFRAC; \
                         sump; \
                         sumt Outputname=mrbayes_out Conformat=simple; \
                     end;" \
                && echo $COMMAND >> mrbayes_in; \
            ) && \
            RUN_IN_WINDOW(( ($ARBHOME/bin/mb mrbayes_in || STOP_ON_FAILURE(MrBayes)) && \
                            NEXUS2NEWICK(mrbayes_out.con.tre,mr_bayes_out.newick) && \
                            $DISPLAY_FUNC));)&

itemhelp:MrBayes.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:Load into ARB ('tree_mrBayes_//'):$ARBHOME/bin/arb_read_tree tree_mrbayes_$$ mr_bayes_out.newick "PRG=MrBayes FILTER=$FILTER RATE=$RATES"
argchoice:Treetool:treetool mr_bayes_out.newick

arg:NST
argtype:choice_menu
arglabel:Number of substitution types
argchoice:6:6
argchoice:mixed:mixed
argchoice:1:1
argchoice:2:2

arg:RATES
argtype:choice_menu
arglabel:Model for among-site rate variation
argchoice:A proportion of the sites are invariable:propinv
argchoice:No rate variation across sites:equal
argchoice:Gamma-distributed rates across sites:gamma
argchoice:Autocorrelated rates across sites:adgamma
argchoice:Mixed invariable/gamma:invgamma


arg:NGAMMACAT
argtype:text
arglabel:Number of rate categories for the gamma distribution\n(Range [0 .. n])
argtext:4

arg:NGEN
argtype:text
arglabel:Number of cycles for the MCMC algorithm
argtext:100000

arg:NCHAINS
argtype:text
arglabel:Number of chains
argtext:4

arg:TEMP
argtype:text
arglabel:Temperature parameter for heating the chains
argtext:0.5

arg:SAMPLEFREQ
argtype:text
arglabel:Markov chain sample frequency
argtext:500

arg:BURNINFRAC
argtype:text
arglabel:Fraction of samples that will be discarded\nwhen convergence diagnostics are calculated [0..1]
argtext:0.25


in:TmpInputFile
informat:genbank
insave:

//------------------------------------------------------------------------------------------


item:MrBayes (custom)
itemmeta:c
seqtype:*
itemmethod:(GOTO_LOCAL_DIR; \
            GEN_NEXUS(mrbayes_in) && \
            PREPARE_MRBAYES_INFILE(mrbayes_in) && \
            ( \
                `# append the mrbayes command block to the nexus file`; \
                cat $COMMAND_FILE >> mrbayes_in; \
            ) && \
            RUN_IN_WINDOW(( ($ARBHOME/bin/mb mrbayes_in || STOP_ON_FAILURE(MrBayes)) && \
                            NEXUS2NEWICK(mrbayes_out.con.tre,mr_bayes_out.newick) && \
                            $DISPLAY_FUNC)))&

itemhelp:MrBayesCustom.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:Load into ARB ('tree_mrBayes_//'):$ARBHOME/bin/arb_read_tree tree_mrbayes_$$ mr_bayes_out.newick "PRG=MrBayes(custom) FILTER=$FILTER RATE=$RATES"
argchoice:Treetool:treetool mr_bayes_out.newick

arg:COMMAND_FILE
argtype:filename
arglabel:MrBayes command file

in:TmpInputFile
informat:genbank
insave:

//------------------------------------------------------------------------------------------

item:TREEPUZZLE ...
itemmeta: T
seqtype:*
itemmethod:(GOTO_LOCAL_DIR; GEN_PHYLIP(infile) && \
            RUN_IN_WINDOW(((puzzle || STOP_ON_FAILURE(puzzle)) && $DISPLAY_FUNC));\
            RM_LOCAL_FILES(TmpInputFile outdist) )&
itemhelp:treepuzzle.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:ARB ('tree_puz_//'):arb_read_tree tree_puz_$$ outtree "PRG=PUZZLE FILTER=$FILTER PKG=strimmer/v. haeseler"
argchoice:Treetool:treetool outtree

in:TmpInputFile
informat:genbank
insave: