Where Methods Disagree


NOTE: in the following, in almost all datasets, base compositions are identical and there are no transversions - as such the Jukes Cantor model is the only appropriate model

The first eight characters are all autapomorphies in the cladistic sense


one   AGGACTTC
two   GAAGTCCT
three GGAATTCC
four  GGAATTCC

parsimony prefers no tree
ML prefers no tree
one AGGACTTC C two GAAGTCCT T three GGAATTCC C four GGAATTCC T parsimony prefers tree II ML prefers tree II
one AGGACTTC A two GAAGTCCT A three GGAATTCC G four GGAATTCC G parsimony prefers tree III ML prefers no tree (or tree II if F81)
one AGGACTTC A C two GAAGTCCT A T three GGAATTCC G C four GGAATTCC G T parsimony prefers trees II and III ML prefers tree II
one AGGACTTC AT CA two GAAGTCCT AT TG three GGAATTCC GC CG four GGAATTCC GC TA parsimony prefers tree III ML prefers trees I and II
Here, transversions are possible, but everyone is different at all sites one ACGT two CGTA three GTAC four TACG parsimony prefers no tree ML (K2P estimating ti:tv) prefers tree II
Here, there are unequal base compositions but all characters
are autapomorphic or constant one AGAGAGAGGGGGGGGGAAAAAAAAAAAA two GAGAGAGAGGGGGGGGAAAAAAAAAAAA three TTTTTTTTGGGGGGGGAAAAAAAAAAAA four CCCCCCCCGGGGGGGGAAAAAAAAAAAA parsimony prefers no tree ML (F81 estimating base comps) prefers tree II