item:AxML + FastdnaML
seqtype: N
itemmeta: A
itemmethod:(GOTO_LOCAL_DIR ; \
            arb_export_rates --arb-notify "$RATES" "T 2.0" "Y 1" "$QUICKADD" | GEN_FASTDNAML(infile) && \
            RUN_IN_WINDOW((cp infile last.infile; time arb_fastdnaml $PROGRAM && $DISPLAY_FUNC)); \
            RM_LOCAL_FILES(TmpInputFile last.infile) )&

itemhelp:dnaml.help

arg:RATES
argtype:weights
arglabel:Select a Weighting Mask
argchoice:POS_VAR_BY_PAR

arg:PROGRAM
argtype:choice_menu
arglabel:Select program to use
argchoice:AxML:axml
argchoice:FastdnaML:fastdnaml

arg:QUICKADD
argtype:choice_menu
arglabel:Use Quickadd
argchoice:Yes:
argchoice:No:Q

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:ARB ('tree_fml_...'):arb_read_tree tree_fml_$$ treefile "PRG=$PROGRAM FILTER=$FILTER RATE=$RATES"
argchoice:Treetool:treetool treefile

in:TmpInputFile
informat:genbank
insave:

