item:FastTree2 (nucleotide) itemmeta:F seqtype:N itemmethod:(GOTO_LOCAL_DIR; \ 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: