TREE SEARCH,,,
Program,Version,Non-default arguments,
TNT,64-bit with no-taxon limit,log tnt.log ; mxram 40000 ; nstates dna ; taxname+80 ; proc matrix.nex ; hold 1000000 ; xmult= replications 100 ratchet 50 drift 20 fuse 5 ; mult 100 =tbr spr ; tsave *mpts.tre; taxname= ; tplot ; save ; tsave/ ; length ; tsave *consensus.tre ; nelsen* ; save/ ; tsave/ ;,NA
IQ-Tree,V1.6.1,iqtree -s matrix.nex -q partitions.nex -nt 24 -pre RESULTS_ -st DNA -v -keep-ident -nt AUTO -cptime 300 -m TEST -ninit 1000 -ntop 200 -nbest 10 -nstop 500 -sprrad 10 -pers 0.7 -bb 1000 -wbtl -nm 1000 -nstep 1000 -alrt 1000,NA
BEAST,V2.4.8,beast -seed 1517922484830 -resume -threads -1 -beagle -beagle_CPU configuration.xml,Change seed accordingly. See .xml file on the Supplementary Material online.
MULTIPLE SEQUENCE ALIGMENT IN GENEIOUS v8.1.9,,,
Program,Parameters,,
Global alignment,"Global alignment, 70% similarity (IUB (5.0/-4.5)",,
Translation alignment,"PAM100-PAM250, gap open penalty = 12, gap extension penalty = 3, refinement iterations 2",,
Mafft,"FFT-NS-i x1000, 200PAM / k=2, gap open penalty = 1.53, offset value = 0.123",,
Muscle,Default parameters,,
Clustar,Default parameters,,