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MDU-PHL / arbow

Cultivate your multiple sequence alignments to get better trees
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Supporting iqtree2: option mapping provided here #11

Closed tseemann closed 4 years ago

tseemann commented 4 years ago 
iqtree -s aln-2020-05-10-175800.aln -pre tree-2020-05-10-175800 -mset HKY,TIM2,GTR -mfreq F -mrate G,R -bb 1000 -alrt 1000 -nt 8 -fconst 8668,5273,5646,9324
-s    same
-pre    --prefix
-mset   --mset
-mfreq   --mfreq                           CHNAGED MEANDING?
-mrate   --mrate
-bb    -B, --ufboot
-alrt    --alrt  
-nt     -T
-fconst   same
-o    same  (outgroup ID)
tseemann commented 4 years ago

iqtree could be v1 or v2 iqtree2 is v2 --version works on both and parses the same

tseemann commented 4 years ago 
  --mfreq STR,...      List of state frequencies

seems to be a different optioon now?

tseemann commented 4 years ago

--mrate STR,... List of rate heterogeneity among sites (e.g. -mrate E,I,G,I+G,R is used for -m MF)

this seems to not work either

qtree2 --mrate F,G --mset HKY,TIM2,GTR Invalid "--mrate" option. (edited) 9:51 iqtree2 --help | grep mrate --mrate STR,... List of rate heterogeneity among sites (e.g. -mrate E,I,G,I+G,R is used for -m MF) 9:51 oh sorry - "F" is not valid, not the --mrate itself 9:51 what is iqtree2 equiv of F ?

andersgs commented 4 years ago

IQTRee2 is now supported as of version 0.6.0